Integrated Pentecostal Ministry of Richard Ngidi in the Apostolic Faith Mission of South Africa

University of South Africa

Integrated Pentecostal Ministry of Richard Ngidi in the Apostolic Faith Mission of South Africa
10.25159/2412-4265/6239Article Mookgo Solomon KgatlePentecostalintegrated ministrysegregated societyApostolic Faith Mission (AFM)Richard Ngidi
Previous studies on the life and ministry of Richard Ngidi only present historical data on his achievements and to some extent his failures. This paper is a sociohistorical analysis that not only reveals historical data but also aims to problematise the data in relation to social problems like racial segregation. A socio-historical analysis is a method that finds synergy between historical and social factors. The socio-historical analysis in this paper juxtaposes the history of Ngidi with racial segregation. The analysis of the ministry of Ngidi in the Apostolic Faith Mission (AFM) of South Africa demonstrates that his ministry was an integrated one amid a segregated society. Integrated ministry refers to a ministry that is able to bring unity in the midst of various divisions in society. The AFM of South Africa, like many other denominations, was a segregated society because of the influence of South African politics on ecclesiastical politics during apartheid. Similarly, many pastors adhered to the racial policies of that time or broke away to start their own ministries. Ngidi was an exception because his ministry was multi-racial, non-political, gender-inclusive, interdenominational and international. Therefore, this paper contends that Ngidi serves as a model for social cohesion and unity in diversity.

Introduction

Before democracy in 1994, South Africa was segregated into different racial groups. Racial segregation was an economic policy for societal advantage through political, ideological and administrative strategies. Sibeko and Haddad (1997, 83) add that the system of apartheid guaranteed that the white minority controlled political, economic and cultural power. Social deprivation was heightened even further by the policy of 2 separate development, resulting in the forced removal of millions of people from their homes. A restrictive urbanisation policy directed towards African people was implemented through pass laws and influx control measures. According to De Wet (1989, 164), the laws and policies of racial segregation influenced the church in a negative way. In the Apostolic Faith Mission (hereafter AFM) of South Africa, a paternalistic policy, undergirded with racial overtones, was sometimes forced upon the church by the state. To a certain extent leaders in the AFM were stimulated by societal and racial mind-sets in addition to practices in the country at that time, and they selfgenerated separation for reasons of language and cultural differences (Venter 2009, 319). The socio-political context of South Africa at that time caused the leaders of the AFM to take decisions that were not biblical, but political.

The AFM was not alone in following racial segregation during apartheid in South Africa. Other Pentecostal denominations followed suit and were racially segregated. Within the AFM, most pastors followed the racial policies of apartheid in South Africa. In this paper the argument is that the ministry of Richard Ngidi  in the AFM was different from other ministries. It was an integrated ministry amid a segregated society. The argument will be demonstrated by the study on the early life of Ngidi in order to understand his family background, work and church affiliations. The ministry of Ngidi in and outside the AFM is studied in detail. However, special attention will be given to his participation and leadership roles in the AFM; enrolment at the Bible school; and his ministry of divine healing, signs and wonders. Ngidi was not a lone ranger in ministry, therefore it is equally important to look at the influences around his life like William Duma and Nicholas Bhengu. The purpose of this article is to demonstrate that the ministry of Ngidi was an integrated one. The outcome of this article has implications for church history today because it helps historians to not only study history from historical data alone, but to also consider social factors.

Methodology and Framework

This paper uses a socio-historical analysis to demonstrate that the ministry of Ngidi was an integrated ministry. Socio-historical analysis is interested in the historical experiences of the past and the social aspects of that historicity. In addition, it is interested in the social groups of that history such as family, church, army, nation or any other group. In this context, it is interested in not only the life and ministry of Ngidi, but also the churches he operated in like the AFM and the American Board Mission. Thus, it is interested in the social conditions in a specific community or society. Sociohistorical analysis links the social aspects of history with the historical data of the specific field. Moreover, the use of socio-historical analysis can help us to reach a more in-depth understanding of the nature of historical aspects discussed within the paper (Costa-Souza, Vieira-da-Silva, and Pinell 2018, 1). Therefore, the socio-historical analysis of this paper will go a long way to studying the life of Ngidi through the lenses of social aspects. The analysis will also assist in combining the history of Ngidi with the challenges of racial segregation that did not only exist then, but are still problematic 3 today. The socio-historical analysis will direct this paper in arriving at the conclusion that Ngidi's ministry was an integrated one. However, before this is done there is a need to explain the essence of integrated ministry.

Integrated Ministry

Integrated ministry is a ministry whereby people from different backgrounds are able to come together and are able to work with situations and people they are not familiar with. This requires people to come out of their comfort zones in order to enter unfamiliar territories. The challenge of integrated ministry is cultural differences that exist among communities. In order to deal with cultural differences, an integrated ministry uses tools like "unity in diversity" to unite people of different backgrounds to come together in life. Thus, the challenges of integrated ministry can be addressed by the coming together of people who-even when they have differences-agree because of their common vision (Rubinstein, Keller, and Scherger 2008, 1). Therefore, while challenges like racial segregation are real and factual, integrated ministry is a well-grounded tool that is able to have an impact on negativity in ministry. Integrated ministry overpowers problems of dividing people according to their race, skin colour, ethnicity, and other forms of divisions. Nonetheless, the attempts of those who are negative in order to keep the people divided in the world cannot be ignored in life. Hence, integrated ministry endeavours to improve on its efforts to minimise the challenges of divisions and to keep people united at all costs (Harmer 2008, 1). In this paper, integrated ministry is not only about unity in diversity but includes other aspects like multi-races, gender-inclusivity, inter-denominationalism, multi-nationalism, and the welcoming of different political views.

The Early Life of Ngidi

Family Background

The Ngidi family played an important role in the AmaQadi clan, which forms part of the Zulu Kingdom. After King Shaka's assassination they became second on the list, so they migrated to S'bubulungu in an area to the north of Durban, within KwaZulu-Natal. The other families in the clan respected the Ngidi family so much that they were involved in the decision-making body of the clan. According to Khathide (2010, 26), Richard Ngidi's father, Bhekinyanga Ngidi, was the son of Mbali Ngidi, who was one of the people who fetched chief Mqhawe during the time when the AmaQadi (clan) did not have a chief. This action of Mbali Ngidi and others endeared them to the hearts of the clan. In the clan, the Ngidi family was held in high esteem. Richard Ngidi (hereafter Ngidi) was born on 6 January 1921 at UMzinyathi in the district of Emaqahadini, Natal. Ngidi's mother gave him the name, Sihlobosenkosi (the friend of the Lord), seven months before he was born when she dedicated her son to the Lord for his service. Ngidi received his primary and secondary education at Inyoni and Inanda, Natal. His father died when he was 17 and as the eldest son, he became responsible to care for his family (De Wet 1989, 139). Ngidi was proud of his cultural heritage.

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The poor family background of Ngidi did not deter him from seeking an education. Ngidi placed the value of education at the forefront and he pursued it at all costs. Ngidi attended Sastri College in Durban before being employed as clerk by African Explosives. On 30 July 1943, he married Regina Mtwana Mbambo. However, some time after their marriage she became ill and suffered from severe attacks of asthma for 12 years. Eight of their children also died while young. During 1952, Ngidi surrendered his heart and life to Christ. According to Khathide (2010, 29), Ngidi was converted to Christianity during one of Nicholas Bhengu's evangelistic crusades (Back to God) in 1952 in Lamontville, Durban. He was then baptised in water by the man of God, William Duma, whose gift was also that of faith in signs and wonders. Ngidi was then baptised in the Holy Spirit and had a Pentecostal experience of speaking in tongues. The practice of speaking in tongues was common among Pentecostals during Ngidi's time. Consequently, Ngidi had to face challenges in his local church because of the hand of God that was upon his life and the exposure to ministries that demonstrated the power of God.

American Board Mission

Ngidi and his family were part of the American Board Mission (ABM). The ABM was started in South Africa when the Rev. Daniel Lindley and his wife, Lucy, came to South Africa in 1835, as one of six couples sent by the ABM to start mission work in the country. Working at first in what is today the North-West Province the Lindleys joined the Grout and Champion families who had opened ABM stations in Natal (ENanda 2013). There was a mission station of the ABM, a satellite of the main Inanda mission station, where the missionaries encouraged parents to have their children educated. Realising this opportunity, Ngidi's parents sent him to primary and higher primary school (Burger and Nel 2008, 252). Ngidi, as a young convert full of the Holy Spirit, was given an opportunity to minister the word of the Lord to the congregation. According to De Wet (1989, 140), each time Ngidi was given an opportunity to preach at the ABM church, he would make use of the time to preach salvation and deliverance in Jesus Christ and he would challenge his fellow parishioners to turn from the works of darkness and wickedness to the kingdom of light. He told the people that as "followers" of Christ their deeds had to conform to the standards and teachings of the gospel of Jesus Christ.

Not only did Ngidi preach morality and encouraged the congregants to repent from their evil ways, he also preached Pentecostal messages and prophesied to the congregants. According to Khathide (2010, 35), what intensified the matter was that Ngidi was beginning to experience the stirrings of the Holy Spirit within his soul. To him it was not a shame to flow in the leading of the Holy Spirit, even at the conferences of the church. In one of the conferences in 1954, Ngidi started to speak prophetically to the people. The Spirit of the Lord was dealing with people in an amazing way. According to Burger and Nel (2008, 254), given these experiences in the ABM, the leadership of the church accused Ngidi and his nephew Alpheus of unorthodox ways of preaching and their family ultimately left the church in 1956. New wine could not be contained in old wineskins and the family started a new church without naming it, as they were looking for a church to which they could affiliate. The ABM asked the local chief to compel this new church to disband, but the chief and his indunas (tribal leaders) resolved that it was unethical for the church leadership to take their members to the traditional court.

The Ngidi family had overstayed their welcome in the ABM. The treatment they received at the ABM demanded their departure. Khathide (2010, 38) explains that the reason why Ngidi and Alpheus stayed longer in the church of the ABM was that they hoped that renewal would come from within. However, at times, it does not help to stay in the hope that the situation will change. Like many leaders in church history who had hoped to renew their churches from within but had failed, so Ngidi and Alpheus had slim chances of renewing their local church from within. They finally decided to leave in 1956. Khathide (2010) continues to say that the new decision was not without challenges. First, the leadership issue had to be resolved. By this time, the group had grown to be large in number. Though the core was still the Ngidi family, the group had attracted quite a number of followers. Ngidi was more gifted but younger than Alpheus and felt that it was traditionally correct for Alpheus to take the lead of the body of believers. The feeling was that Alpheus, being older, was more experienced to lead them.

Influences on Ngidi

Ngidi was not a lone ranger in ministry, but believed in collaboration with other ministers of gospels that upheld a similar vision. The life and ministry of Ngidi were influenced by many personalities. Among those who had a positive influence on the life and ministry of Ngidi, is Nicholas Bhengu. Bhengu was one of the most successful twentieth-century Pentecostal church leaders in South Africa. Many scholars recognise him as one of the generals of African Pentecostalism. While living in Lamontville in Durban in 1956, Ngidi attended a gospel crusade of Bhengu's "Back to God" gospel team. Bhengu was not very demonstrative in his preaching, but when he prayed for people, the power of God was demonstrated with sick people being healed and the spiritually oppressed being set free (Burger and Nel 2008, 253). Bhengu introduced Ngidi to the power of the Holy Spirit. He lectured him on the working of the Holy Spirit. He told him that anyone filled by the power of the Holy Spirit was capable of doing works of power. It was this meeting with Bhengu that catapulted Ngidi into evangelistic and healing ministry, in which he became the greatest evangelist in the AFM (Lephoko 2005, 97).

The healing aspect of the ministry of Ngidi comes from one of the African Pentecostals who featured mightily in the area of healing miracles, namely Rev. William Duma. Duma was one of the most dynamic Baptist preachers in South Africa, as well as being renowned for his healing and prayer ministry. What amazed Ngidi was that Duma was not educated like pastors Bhengu, Letwaba and others, yet miracles and healings in his ministry took place regularly. Even today, there are many ministers of the gospel who fall in the category of Duma, that is, they are not educated but they proliferate in signs and wonders. However, this aspect should not be used to discourage ministers from studying or being educated in their life. What surprised Ngidi further was that even white people and Indians would flock to the Baptist Church in Lamontville to listen to Duma preaching his famous sermons in "broken" English. Thus, the ministry of Duma to some extent was also inclusive of all races. Ngidi realised that it was not language proficiency that was needed to perform miracles but the anointing of the Holy Spirit, since he was also encouraged to go out there and demonstrate the same power of the Holy Spirit (Khathide 2010, 54).

The Ministry of Ngidi in the Apostolic Faith Mission

Ngidi joins the AFM After the Ngidi family had been excommunicated by the ABM in 1956, the family fellowshipped together without a church name or denominational affiliation. According to De Wet (1989, 140), one day-after a time of fasting and prayer-Ngidi had a dream of a golden road leading to heaven, with the letters AFM written on it. Ngidi looked for such a church, but was unsuccessful because the AFM had only a small membership among blacks in Natal. The family then sent a delegation, where they met pastor Amos Mthiyane, who led an AFM assembly in Durban with several satellites. Mthiyane visited UMzinyathi and welcomed the new church of the Ngidi family into the AFM. At last, Ngidi and his family were happy to join the AFM after a long time of struggling. After this welcome, the Lord's Communion was served. Ngidi, together with the whole family, attended their first AFM district conference (Khathide 2010, 54). It must be noted, however, that at that stage the AFM in Natal had strong Zionist tendencies with unorganised meetings and customs derived from the Old Testament. The liturgy was not appealing to Ngidi, but he believed and was convinced to join the AFM. Besides, the Zionist tendencies were not peculiar to the AFM in Natal but were part of the black section of the AFM and evident in many assemblies (Burger and Nel 2008, 255).

Ngidi Joins the Bible School

In response to his calling, Ngidi was admitted in 1962 to the Leratong Bible School in Lady Selborne. He completed his training, was accepted as a pastor of the AFM during 1963, and was ordained on 19 March 1965. He served the church loyally, faithfully and uninterruptedly until he was called to glory (De Wet 1989, 140). At the college, Ngidi always wore a tie as a sign of respect for the ministry, and his wife and he studied Scripture with great seriousness. While still attending classes, he was elected as secretary for the Natal District Council, showing the confidence of his people in his abilities (Burger and Nel 2008, 255). Ngidi knew that God's work could be done effectively only if he was thoroughly trained. Under the able tutorship of pastor Cooksey, Ngidi was prepared for a ministry that would change and bless countless numbers of people across this country and beyond. It was at this Bible college that his Pentecostal convictions were consolidated (Khathide 2010, 45). This is amazing with regard to the ministry of Ngidi, because he was already used by God but was willing to sit and be taught by others. The failure of many anointed men of God is that, unlike Ngidi, they cannot sit under other leaders and be thoroughly trained and equipped for the work of ministry.

Leadership roles of Ngidi

When Ngidi had completed his studies at Leratong Bible School, he needed to find a church where he could pastor on a full-time basis. The normal practice is that after the completion of one's qualification, the minister is now ready to pastor a local assembly on a full-time basis. According to Khathide (2010, 51), after prayer and consultation, the AFM Natal district officials resolved to send him to one of the underdeveloped places of Pietermaritzburg. At times, superiors in denominations have a propensity of sending unqualified pastors to assemblies that cannot support them. This was the case with Ngidi. He was assigned to an assembly that had no existing structures and was expected to hit the ground running. There was no groundwork there to support him. Ngidi and his wife had to find a congregation with the help of God. The Ashdown assembly was started with only one believer. On the first Sunday, only four people were present in the mud building where the service was held. Ngidi was not deterred. He preached from well-prepared notes. He preached from his heart as if preaching to thousands. At Bible College, he had been taught that if he could not preach to one he could not preach to a multitude.

However, it seems that God had bigger plans for Ngidi than the challenges he went through in his first assembly with the AFM. Contrary to AFM church rules at that time, Ngidi was elected as secretary of the Natal district council. The reason for this assertion is that Ngidi was still very much at the beginning of his career in ministry and was actually still expected to lead at an assembly level. The confidence shown by the people in electing him, really amazed Ngidi but this did not make him arrogant. He was determined to serve the church and the Natal region with everything he had. In addition, Ngidi was a member of the executive council of the AFM for five years and was reelected as such during March 1985, just a little less than two months before he died. He became the first black vice-chairman. Because of his fatherly portrait in the church, Ngidi withdrew from the church court, a body that dealt with discipline in the church. In Natal, Ngidi was vice-chairperson, eventually becoming chairperson of the work there. Under his supervision, the work grew in leaps and bounds (Burger and Nel 2008, 255).

The significance of Ngidi's ministry and leadership in the black section of the AFM is especially evidenced in the following. Firstly, the emphasis he placed on evangelism and his successful evangelistic campaigns, especially tent-campaigns, enthused the black pastors of the AFM and a new wave of evangelism swept all over South Africa. Secondly, Ngidi's teaching and example of regular fasting and prayer inspired other pastors to follow his example. Thirdly, Ngidi's practice and success in praying for the healing of the sick caused many pastors to model themselves after him. Fourthly, Ngidi never allowed any discussion about politics, of any nature, in any meeting in which he was present (De Wet 1989, 140). Ngidi was a very humble leader. He was a model of servant leadership to other pastors in and outside the AFM. In addition, Ngidi was an accessible leader and full of love. One of the stunning things in Ngidi's character, according to Khathide (2010, 85), was that he seemed to have a perennial capacity to love people. He made sure that he knew his congregants by name. He had room for each one in his big heart. His welcoming heart was so big that many pastors felt accommodated in his life. Even those people who tried to give him a tough time in the congregation were always sure of his forgiveness and unconditional love.

Fasting

Many perceive fasting in Pentecostalism as one of the ways to access greater power, after which the minister of the gospel is able to perform greater works. In addition, fasting is perceived as a form of receiving direction, especially when one is about to take major decisions in life. Therefore, fasting is a tool to give a minister a major spiritual boast to operate at a higher level in ministry. Sensing the tremendous spiritual need among his people, combined with his desire for more frequent manifestations of the gifts of the Holy Spirit in his ministry, Ngidi fasted and prayed for 40 days (Khathide 2010, 85). He felt called to fast for 40 days when he was 49 years old. He started just before Christmas in 1970. He withdrew to UMzinyathi "to dig for gold," as he described his fast. On the tenth day, he saw a vision of a ball of fire coming from the east at a very high speed. It hit him so hard that it knocked him to his knees. Even his brother's wife, sleeping in the next room, was carried out of her bed due to the impact. After that experience, Ngidi knew he was a different person (Burger and Nel 2008, 255).

For some time, the Lord had been speaking to Ngidi to isolate himself for a period of fasting which would last 40 days and nights. He had not heard of anybody, except Jesus, who had done this before. The fasting and prayer life was taken as part of every Christian then. In the black churches of the AFM in Natal, fasting was emphasised from the pulpit. Fasting was taken as a symbol of dedication to the Lord. Every Christian was expected to fast at least once a week. The idea was to humble oneself in order to get more power to serve the Lord (Khathide 2010, 56). This is one of the distinct aspects of Ngidi's ministry, given the fact that it is not everyone who can fast for 40 days. Even in the Bible, few individuals ventured successfully on this kind of fasting. According to the Bible, only three people fasted for 40 days. The first was Moses; the Bible explains very clearly that in the period he was with the Lord, he did not eat and drink water (Exodus 34:28). The second is Elijah, who received food from the angel of the Lord and after eating, spent the next 40 days and 40 nights without eating (1 Kings 19:8). The third was Jesus Christ, who was led by the Spirit into the wilderness and there He did not eat for 40 days (Luke 4:1-2).

Signs and Wonders

In the days that followed the fast, God performed extraordinary miracles of healing; the success reports state that in one of Ngidi's healing ministries, 10 blind people received 9 their sight. The success of his campaigns is clearly demonstrated by the fact that when Ngidi entered the ministry in Natal and KwaZulu, there were only nine assemblies. This increased under his ministry and leadership to 212 assemblies (De Wet 1989, 140). The full-time workers increased from 13 to 175, the blind saw, the deaf heard, cripples walked and hundreds were filled with the Holy Spirit. Among those healed, was Ngidi's wife Regina who was delivered from asthma (De Wet 1989, 141). Ngidi's wife had been suffering from severe attacks of asthma for 12 years. Regina was healed instantaneously in answer to the prayers of Ngidi. This miracle of the healing of his wife spurred Ngidi on to seek a greater manifestation of God's power (Khathide 2010, 53). God continued to perform miracles in Ngidi's family. One day he had to bury one of his children and he had no money for the coffin and other funeral expenses. He went to a nearby hillock to pray for money. He prayed and when he opened his eyes, he found enough money for funeral expenses on the surrounding ground (Khathide 2010, 42).

Many scholars and pastors regard Ngidi as a miracle worker and the man who moved in power. In the words of Molobi (2014, 9), Ngidi of the AFM was known as the stylish preacher amongst the black people, especially township dwellers. His messages of healing, baptism and conversion, had an emphasis on the Holy Spirit, and they became prominent in the white residential districts. Apodaca (2016) adds that when he went to a new area, he set up a tent. He prayed for God to show His power. It was said of his ministry: they do not advertise services over there. They do not have magazines or radio in that part of the country. So first, Ngidi trusts the Lord to heal a sick person. Soon the people hear about this man praying for the sick. Since they are a needy people, they come and God starts to heal. After preaching, Ngidi would pray for people individually and God would touch them. Different people with their various challenges like blindness, deafness and lameness received their healing. Thus the blind saw, the lame walked and the deaf could hear. The miracles happened because Ngidi trusted God in his ministry and God never disappointed him (Bonnke 2009, 237).

Testimonies in Pentecostalism play a big role in authenticating the miracles that a minister performs in the lives of the people. Thus, repeatedly, people who are healed or have received any kind of a miracle would be asked to testify in front of the congregation. This type of testimony encourages those who are still hoping for a miracle or healing in their lives. One of the testimonies of the people healed in Ngidi's meetings is that of a crippled man, known as Shezi. This man tormented Ngidi for a long time. Ngidi then organised a big healing service at Umkhomazi where Shezi stayed and where he would demonstrate God's power by praying for him. He invited people to bring the sick for prayer and promised that God's power would be available to all. Hordes of people turned up and Ngidi preached a short sermon. He then prayed for all the sick before turning to Shezi, laying his hands on his head he commanded him to walk in the name of Jesus. Shezi stood up and walked. The crowd was amazed and glorified God because this was happening for the first time in their area. Many people gave their lives to Christ because of this miracle (Burger and Nel 2008, 256).

Integrated Pentecostal Ministry

Multi-racial

The ministry of Ngidi was a multi-racial one. This, according to Khathide (2010, 68), is demonstrated by the fact that when Ngidi needed a tent for his evangelistic ministry, two white pastors, Du Toit and Gschwend, played an important role in helping Ngidi obtain the tent and the necessary equipment. These pastors helped raise finances for this great task from other sources, especially from white AFM churches. Khathide continues to say that the meetings in the new tent were multiracial. Some people rolled in the dust. Others stood up to praise God with their hands held high towards heaven. Most of these people, including whites, were crying. In a few other places, people witnessed Ngidi's sense of timing God's power (Khathide 2010, 105). In many other instances, Ngidi continued to work well with people of other races. One of the co-workers in Christ was Reinhard Bonnke who worked with Ngidi for a long time. Ngidi assisted Bonnke in establishing his work in Botswana. Moreover, in the Executive Council of the AFM, Ngidi occupied a leadership position as the only black pastor; the rest of the leaders were white. This demonstrates that the ministry of Ngidi integrated races rather than to segregate them. What is more amazing is that this happened during apartheid in South Africa.

Non-political

There was an influence of South African politics which seeped into ecclesiastical politics during apartheid. However, Ngidi hardly permitted any discussion about politics in the meetings he attended. He knew that such political discussions would hurt white missionaries in the midst of the black church. People like Pastor Edgar Gschwend and a few others would have been able to accommodate such discussions, but the general feeling was that the rest of the missionaries and some older pastors would have found it difficult to go along with (Khathide 2010, 100). Ngidi was not the first AFM black pastor to be silent on politics. Elias Letwaba was also a humble man and remained silent on the politics. Clark (2007, 42) explains that Letwaba was one of the first black leaders of the AFM, a man whose ministry in the northern parts of the country led to the establishment of a large African church. Letwaba was a humble man who accepted the racial indignities imposed upon him by the white church leaders. His influence in the church was his powerfully charismatic evangelistic ministry, and the (mostly ignored) fact that it was his vision that established the first Bible School in the AFM in 1930, namely Patmos Bible School, for the training of African pastors.

Change in the AFM came with the third generation of black pastor Frank Chikane. Chikane was more vocal regarding issues of politics. Anderson (1992, 49) explains that if Letwaba belonged to the first generation of the black Pentecostals of the AFM, and Ngidi to the second, Chikane is an outstanding example of the new third generation of black Pentecostal leaders in South Africa. In this respect, Chikane is in stark contrast to Letwaba and Ngidi, and in fact in contrast with many African Pentecostals in South Africa. Unlike them, Chikane was not raised in a rural environment. He was born in 1951 and raised in the home of an AFM elder, Pastor James Chikane in Soweto, Johannesburg. The silence of Ngidi on politics was informed by his perception that such involvement would cause divisions in the church and affect his ministry. Ngidi did not see a connection between ministry and politics. This worked in his favour because all people, including those who were perceived as anti-black, supported his ministry. However, the context in which many people lived at that time did not work in their favour. Yes, they were saved, healed and delivered in the ministry of Ngidi, but still lived in tough economic and social conditions.

Gender-inclusive

The ministry of Ngidi included women, especially at leadership level. Ngidi was the first to use black women-workers. With 30 well-trained women-workers under his supervision, several new assemblies were established. The AFM in Natal became known as the "Church of Ngidi" because of the impact of his ministry and leadership in Natal (De Wet 1989, 141). The women were supported mainly by free-will offerings taken at conferences in Natal. There were no statutory contributions that could be used, because this was a novel idea in the AFM. These women became a force in the AFM in Natal, fanning revival fires in many regions (Burger and Nel 2008, 258). To Ngidi, women were not just "assistants" in the ministry of evangelism. He accorded them full status of ministry long before the AFM could think of ordaining women. These women would at times conduct gospel crusades alone. They were requested to go to rural places to establish congregations. Under Ngidi's supervision and protection, these women gave their all for the extension of the kingdom of God. These women would start an assembly and Ngidi would come and receive the new converts into fellowship (Khathide 2010, 111).

Inter-denominational

Denominational refers to a ministry that is affiliated or is a part of a well-established denomination. There are well-established denominations in South Africa from both mainline churches and Pentecostal churches. However, the majority of para-churches in South Africa are non-denominational. Non-denominational refers to a ministry that is not affiliated to a specific denomination. Inter-denominational in this context refers to ministry that crosses one denominational boundary into the other without terminating affiliation with the former. The ministry of Ngidi is considered inter-denominational because while at the AFM, Ngidi was also able to work with Christ for all nations. According to Bonnke (2009, 98), "Christ for All Nations" was birthed after he had seen God's miracle-working power in the life of Ngidi; that kick-started the powerful ministry of "Christ for All Nations," which is now known all over the world. Khathide (2010, 111) adds that when Bonnke launched the "Christ for All Nations" church, he felt a great need for the manifestation of the power of God in his evangelistic crusades. As a Pentecostal preacher, he felt that people must not only be preached to at gospel meetings; they were also to be prayed for, for healing from their diseases.

Although Ngidi worked with other churches like "Christ for All Nations," Khathide (2010, 95) argues that most of Ngidi's work took place within the AFM. This could be attributed to several factors. Firstly, Ngidi was a very loyal person; although he connected with other churches he remained loyal to his church and made sure that he served the church with diligence. The researcher believes that further opportunities could have arisen in the ministry of Ngidi to join other ministries or churches, but he remained loyal to his church. It must be noted that Ngidi remained loyal when many black pastors in the AFM were undermined and could not take leadership roles. Second, it could have been his educational and theological background that limited him from expansion. However, this reason is somewhat problematic, given the fact that many during Ngidi's time expanded their ministries, regardless of their education. One obvious example is William Duma, who touched many people but was not as educated as leaders like Nicholas Bhengu. Third, there would have been tremendous administrative constraints. Fourth, it could be that Ngidi was convinced beyond reasonable doubt that his calling was in the AFM and in Natal specifically.

International

An international ministry refers to the ability of the minister to cross the borders of his country to a level of going oversees into the global north countries. It is not every minister who has this ability or grace to cross the borders or even go overseas into Europe, Asia, America and other continents. The ministry of Ngidi crossed the border of South Africa. This illustrates that his ministry was an international one. It was not only concentrated in Natal, but rather went beyond its original locality. He ministered in several other parts of southern Africa as well as in Europe (De Wet 1989, 141). In order to take the ministry of Ngidi to an international level, the first step, it was agreed, would be to take Ngidi to Zimbabwe. Pastor Gschwend, the AFM director, arranged with the AFM in Zimbabwe for Ngidi to minister at the Rufaro national conference (Khathide 2010, 95). In addition, Ngidi and Gschwend, together with their wives, set out for Europe to preach the gospel of Jesus Christ. They conducted meetings in Switzerland (Zurich) and France (Reins and Strassburg). The gospel meetings were successful, especially in France (Khathide 2010, 117).

The Last Days of Ngidi

On Friday 4 May 1985, during the early afternoon Ngidi became unconscious. The nursing sister in his congregation who had been alerted of his condition advised that he be rushed to the hospital. When he arrived at the Edendale hospital, he was diagnosed to be in a diabetic coma. At 13:00 Ngidi answered the Lord's final call. Leaving his wife, three daughters, one son, and four grandchildren, Ngidi was no more. More than 8 000 people attended his funeral. This number indicates how many people loved and followed the ministry of Ngidi until his death (Khathide 2010, 84).

Ngidi made a significant contribution as a minister and an evangelist within the AFM in areas of church planting, pastoring, mass evangelism, prayer movement, healing 13 ministry, the encouragement of women participation in ministry, and the growth of Pentecostalism (Mathole 2005, 184). Ngidi never believed in a large congregation for himself. Because of the blessing of the Lord on the Imbali congregation, people came from all over to be its members. Ngidi could have easily led a congregation of several thousand at the time of his death, but he decided against it because he believed in empowering other leaders, especially women (Khathide 2010, 84).

Conclusion

This paper studied the life and ministry of Ngidi by using a socio-historical analysis. The life and ministry of Ngidi have been juxtaposed with one of the problems that are persistent in society, namely racial segregation. The AFM was a segregated society because of the apartheid policies of that time. The AFM was not alone; other denominations followed suit and supported racial policies prevalent at that time. Many pastors in the AFM succumbed to the South African politics during apartheid. Through a socio-historical analysis, this article has demonstrated that the ministry of Ngidi was an integrated one in a segregated society. The ministry of Ngidi was multi-racial because both black and white people attended his services. He was non-political because he perceived politics as a divisive mechanism during apartheid. Ngidi was the first AFM pastor to recognise the ministry of women. Moreover, the ministry of Ngidi crossed denominational boundaries. Lastly, Ngidi went as far as Europe to preach the word of God. The ministry of Ngidi remains a model for social cohesion and unity amid diversity. This study on the life and ministry of Ngidi changes the way we study church history, because history was studied here by also considering underlying social aspects such as racial segregation and discrimination against women.

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The United Congregational Church of Southern Africa Commemorates People who Made a Remarkable Contribution to Inanda. Enanda Online, ENanda Online. 2013. "The United Congregational Church of Southern Africa Commemorates People who Made a Remarkable Contribution to Inanda." Accessed February 4, 2013. www.enanda.co.za.

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Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach
2020

Umair Ilyas
Shahiq Uz Zaman
Reem Altaf
Humaira Nadeem
Syed Aun Muhammad
Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach

J of Biol Res-Thessaloniki
278202010.1186/s40709-020-00118-1RESEARCH This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article' s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article' s to the data made available in this article, unless otherwise stated in a credit line to the data.Colorectal cancerMicroarraysFunctional genomicsPPI networkBiomarkers
Background: Colorectal cancer is known to be the most common type of cancer worldwide with high diseaserelated mortality. It is the third most common cancer in men and women and is the second major cause of death globally due to cancer. It is a complicated and fatal disease comprising of a group of molecular heterogeneous disorders.Results: This study identifies the potential biomarkers of CRC through differentially expressed analysis, system biology, and proteomic analysis. Ten publicly available microarray datasets were analyzed and seven potential biomarkers were identified from the list of differentially expressed genes having a p value < 0.05. The expression profiling and the functional enrichment analysis revealed the role of these genes in cell communication, signal transduction, and immune response. The protein-protein interaction showed the functional association of the source genes (CTNNB1, NNMT, PTCH1, CALD1, CXCL14, CXCL8, and TNFAIP3) with the target proteins, such as AXIN, MAPK, IL6, STAT, APC, GSK3B, and SHH.Conclusion:The integrated pathway analysis indicated the role of these genes in important physiological responses, such as cell cycle regulation, WNT, hedgehog, MAPK, and calcium signaling pathways during colorectal cancer. These pathways are involved in cell proliferation, chemotaxis, cellular growth, differentiation, tissue patterning, and cytokine production. The study shows the regulatory role of these genes in colorectal cancer and the pathways that can be effected after the dysregulation of these genes.
 Ilyas et al. J of Biol Res-Thessaloniki (2020) 27:8
been developed [2]. Numerous risk factors are known to be associated with the progression of CRC with 95% of cases having adenocarcinomas. This includes enhanced alcohol intake, reduced physical exercise, a poor diet plan that is rich in fats and poor in fibers, personal or familial history of polyps, age greater than 50, and inflammatory bowel disease [3].

Following the development of colorectal carcinoma, the subsequent genetic and epigenetic alterations in specific oncogenes and/or tumor suppressor genes of gastrointestinal epithelial cells causes it to undergo cell proliferation and self-renewal, triggering the normal epithelium to be hyperproliferative mucosa. This results in a benign adenoma that eventually grows into carcinoma and in about 10 years becomes metastatic [4].

The normal epithelial cells of the gastrointestinal tract are arranged along a crypt-villus axis. The undifferentiated pool of colon stem cell and progenitor cells having the ability of self-renewal and pluripotency are found at the bottom of the crypt. These cells while moving along the axis undergo differentiation in all epithelial colon lineages. Whilst these cells arrive at the top of the axis which usually takes 14 days they result in apoptosis. Several proteins are known to be involved in the regulation of this process such as BMP, Wnt, and TGF-β [4]. The onset of CRC has shown the involvement of various altered molecular signaling pathways that may result in the resistance to anti-tumor agents. These pathways include the Wnt/APC/β-catenin, transforming growth factor-β (TGF)-β/Smad, phosphoinositide 3-kinase (PI3K)/AKT/glycogen synthase kinase-3B and NF-κβ.

The diagnosis of CRC plays a pivotal role in the early prediction of CRC. If detected early it can be treated with surgery alone, however, in metastatic disease along with surgery chemotherapy is included. Presently, the prediction of CRC is based on the classification of the American Joint committee on Cancer (AJCC), TNM staging. But because each stage is a heterogeneous group of disease it is difficult to relate the TNM staging with prognosis. A more rapid and cheaper form of molecular characterization of cancer has become possible with the advancement of NGS technology. Most of the genetic biomarkers have gained a clinical value as a prognostic or therapeutic marker such as the MSI and the EGF signaling pathway [4].

To get a clear picture of the carcinogenesis, tumor growth and metastasis of colorectal cancer, the microarray analysis has been proved useful to gather information on thousands of genes at a time. The genomic alterations occurring in colorectal cancer can be identified by microarray analysis which can help in the diagnosis, characterization, and treatment of colorectal cancer [5]. However, certain challenges are still faced in the application of microarray assays according to some studies. One approach to overcome such challenges is to utilize the online Gene Expression Omnibus (GEO) database. This database can assist in increasing the size of the sample, statistical power and sample heterogeneity [6][7][8].

The aim of this study is to screen out significant CRC associated genes that can act as candidate biomarkers to detect early cancer and to elucidate the pathogenesis of CRC. The differential expression analysis of ten microarray datasets was performed to identify the candidate genes based on significant scoring function. The expression profiling of these genes was also performed to determine the expression patterns of these potential markers in several tissues. Cluster analysis and Functional enrichment analysis was employed to confirm the function and association of shortlisted genes in causing CRC. The protein-protein interaction and pathway analysis confirmed the association of candidate genes with colorectal cancer and the regulation of Wnt, NF-κβ, and MAPK. The search for new predictive, diagnostic and prognostic biomarkers in colorectal cancer is of great importance and has become the goal of biomedical research on CRC. The study will aid in the biomarker discovery by getting valuable insights through studying these molecular networks that can be used in public datasets for better outcomes in other diseases as well.

Methods

Accession of gene expression data

The aim of this study was to identify potential targets for colorectal cancer. The gene expression datasets of colorectal cancer were accessed from the Gene Expression Omnibus database under two screening conditions (organism: Homo sapiens, experiment type: expression profiling by an array). Each dataset comprises of GEO accession number, platform, sample type, number of samples and gene expression data. The array platform used was Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (CDF: Hs133P_Hs_ENST, version 10) (Affymetrix, Inc., Santa Clara, CA, 95051, USA, Technology: in situ oligonucleotides). In order to detect the gene expression, the array platform and the annotation information (hgu133plus2) of probes were used. Computational analysis was performed using R and BioConductor packages containing AffyQCReport, Affy, Annotate, AnnotationDbi, Limma, Biobase, AffyRNADegradation, hgu133plus2cdf, and hgu133a2cdf.

Preprocessing and differential expression analysis of microarray datasets

The phenodata files were prepared for each dataset in a recognizable format [9]. The normalization of the data was done using Bioconductor "ArrayQuality Metrics"  [10][11][12]. This was done to compare the microarray data sets. The background correction for perfect matches (PM) and mismatches (MM) was performed by the Robust Multi-array Analysis (RMA) in order to remove local noise and artifacts [9]. Perfect matches (PM) and mismatches (MM) was calculated using the following equation.

where, PM is a perfect match, Background (BG) caused by optical noise and non-specific binding (S); ijk is the signal for probe j of probe set k on array i.

The background (BG) and the signal expression (E) forms the PM-data. The dataset normalized to median level expression was analyzed by the "Array Quality Metrics" package of Bioconductor software [10][11][12]. Expression value having a p-value < 0.15 was considered marginal log transformation. For each dataset, the genegene covariance matrix was calculated across all array (54675 Affyids) using the following formula.

where F1 and F2 are distribution functions of the actual and reference chips, respectively.

To attain the summary of intensities the RMA-algorithm was used to calculate the averages between probes in a probe set.

The degradation analysis to measure the quality of RNA in these datasets, AffyRNADegradation package of Bioconductor was used (Affymetrix, 1999(Affymetrix, , 2001. The pairwise comparison was done to identify the DEGs in each dataset and for multiple testing correction Benjamini-Hochberg method was employed. The differentially expressed genes were shortlisted along with measurement of quality weights. The shortlisted genes were ranked according to their p values and the resulting scores. Significant cut off values was set to calculate the moderated statistics with p-value ≤ 0.05, FDR < 0.05 (false discovery rate), absolute log fold change (logFC) > 1 and FDR < 0.05 (false discovery rate) [13].

Curation of CRC-related genes

The shortlisted DEGs were further screened for colorectal associated genes using diverse data source including PubMed, MeSH, OMIM, and PMC database to filter
PM ijk = BG ijk + S ijk . BG PM ijk = E S ijk | PM ijk > 0. S ijk ∼ Exp ijk BG ijk ∼ N β i , σ 2 . X norm = F 2 −1 (F 1(x)).
significant disease specific genes. The cluster analysis [14] was performed based on expression values in each dataset of CRC-related differential expressed genes in order to identify the variations in gene expression levels between treated and untreated replicates using CIMminer tool [15].

Functional enrichment analysis

In order to understand the biological functions of these CRC related genes the Gene ontology, functional annotation and pathway enrichment analysis [16,17] was performed. The web-based tools used for this purpose were DAVID (Database for Annotation Visualization and Integrated Discovery) [18] and FunRich Annotation tools [19].

Protein-protein interaction network

The topology and functional protein interactions are useful to analyze the biological and pathological conditions of a specific disease. The protein-protein interaction helps in identifying these features and the functional relationship of such proteins can be interpreted through genomic associations [17,20]. The PPI network shows the interaction of each protein with a number of other genes with biological or molecular functions having different activity in the pathological state as compared to normal [21]. Proteins that interacted with each other during colorectal cancer were evaluated from STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) [21] and HAPPI databases (Human Annotated and Predicted Protein Interaction) databases [22] with a confidence score of 0.999. Cytoscape software (version 3.2.1) was used to visualize the molecular and network interaction to identify the role of seeder and target genes in CRC [23]. The network showed the role of each target gene signatures that interacted with CRC associated source genes in colorectal cancer. The role was determined by mapping the target gene with seeder genes using, OMIM, MeSH, and PMC databases. The gene mapping determines the potential colorectal related gene signatures to be functionally related whose dysregulation causes a disease phenotype. The total number of target genes interacted with each source protein was calculated. A molecular sub-network of those genes that were associated with pathways of interest causing colorectal cancer was constructed. The topological network properties were calculated using Network Analyzer in Cytoscape [24].

Integrated pathway modeling

The integrated and metabolic networks of CRC-related source genes were analyzed and the Co-relation between test genes was observed. To recognize the underlying pathways involved in the progression of CRC the pathway analysis was performed which could help in identifying the biomarkers of this disease. The curation and mapping of candidate biomarkers were done using KEGG (Kyoto Encyclopedia of Genes and Genomes) [25], Reactome and Wiki pathways. PathVisio3tool was used to reconstruct the cellular and signaling pathways of potential biomarkers [26] and the potential mechanism of each marker in the pathway was studied based on the pieces of evidence available in literature and databases. For cross-verifications, we used TCGA and the Human Protein Atlas databases and analyzed the expression level of ranked DEGs in colorectal cancer.

Results

Microarray analysis and normalization

Ten datasets were downloaded from online GEO database with .CEL format related to CRC. The size of an array of AffyBatch object comprised of 1164 × 1164 and 732 × 732 features with related Affyids (Table 1). In order to avoid the systematic variation, the quantile normalization was used for background correction and normalization. The probe level data obtained after normalization shows the quality of the individual array of each dataset in the MA plots (Fig. 1). The computation of genegene covariance matrix across all arrays was performed by ignoring the missing values in each dataset and to assure they were on a similar scale to log-transform the arrays. In each probe sets, the probes were arranged by location relative to the 5′ end of the targeted RNA molecule. The severity of RNA-degradation and significance level was presented by function plotAffyRNAdeg (Fig. 2) and a single summary statistic for each array in the batch was produced by the function summary of AffyRNAdeg (Additional file 1: Table S1). The list of databases, tools, and software used in this study are available in (Additional file 1: Table S2).

Identification and screening of differentially expressed genes

About 50 DEGs in each microarray dataset were identified by pairwise comparison between biologically comparable groups. From these 50 DEGs, the top 20 genes in each dataset were ranked and selected based on FDR (< 0.05), p-value (≤ 0.05) and logFC (> 1) parameters. And from these 20 genes, seven common genes of each dataset were identified as the potential biomarker candidate (Additional file 1: Table S3).

Data mining and cluster analysis

The seven significant colorectal cancer associated genes shortlisted from the differentially expressed genes were CALD1, CTNNB1, CXCL14, PTCH1, CXCL8, TNFAIP3, and NNMT after mapping with PubMed, OMIM, MeSH, and PMC databases. The role of sorted genes in colorectal cancer was curated and counted ( Table 2). The genetic expression of colorectal cancer cell samples showed a clear difference between the treated and untreated groups (Fig. 3).

Gene enrichment analysis

Significant enrichment was obvious in 5 downregulated and 2 upregulated genes. The clinical phenotypes associated with the dysregulation of these genes are pilomatrixoma, congenital lung cyst and ovarian fibromata (Fig. 4a). The biological processes are related to cell communication, signal transduction, immune response, energy, metabolism and cell growth and maintenance (Fig. 4b).

Gene network analysis

In PPI, a total of 233 nodes and 134 edges were retrieved from STRING [21] and HAPPI database [22] with a confidence score of 0.99. The database showed the interaction of CRC-associated genes with potential other genes that were contributing to a disease phenotype. The network was categorized into three neighborhoods: light pink and red nodes indicate the CRC-associated potential biomarkers while the remaining blue nodes represent the other target proteins. The potential biomarkers were found to functionally interact with other biologically essential target proteins. Some of them are, APC, IL6, MAPK1, NFkb1 and SHH (Fig. 5). The source protein CTNNB1 was shown to be interacting with APC and NNMT showed interaction with CDK38 and STAT3. Similarly, CALD1 is associated with MAPK1 while, PTCH1 shows interaction with a family of hedgehog proteins SHH, IHH and DHH with clinical phenotypes. The network analyzer was used to classify and improve the network performance and to interpret the topological properties of the network. The disease gene mapping of target genes using CTD showed that more than 50 genes have a functional relation with the source/seeder genes in CRC (Fig. 5).

Pathway modeling

The source genes identified were further studied to evaluate the molecular mechanism of these genes in CRC. The network generated after reconstruction showed that several pathways were involved in the pathogenesis of colorectal cancer. Along with the Wnt pathway and the canonical pathway other pathways, the MAPK pathway, Calcium signaling pathway, metabolic pathway and RIGlike 1 receptor pathway have also shown a connection with colorectal cancer (Fig. 6). The gene ontology of these pathways is associated with cell proliferation, chemotaxis, stem cell maintenance, and apoptosis. Therefore,  the progression of CRC is related to the overexpression of genes that leads to cell proliferation and anti-apoptosis and downregulation of genes that inhibit the proliferation and cellular differentiation of cells. The association of differentially expressed genes with colorectal cancer were cross-referenced by TCGA and the Human Protein Atlas. The median expression level of interactive gene signatures and source DEGs is significant in cases as compared to control. The interactive survival scatter plot (Fig. 7) indicates the expression of these DEGs is favorable in colorectal cancer. The pathways and pathological analysis showed that the proteins level is linked with cancer. These interactive survival scatter plots indicated the consequence of RNA and protein levels on clinical  survival. The results showed that individual tumor gene expression patterns differed greatly and could surpass the variability between different types of cancer. Lower patient survival was usually associated with over-expression of genes in mitosis and cell growth and down-regulation of genes involved in cellular differentiation. This data enables the generation of metabolic models in a customized genome scale for cancer patients to recognize important genes of tumor growth.

Discussion

In this study, the DEG for colorectal cancer were identified and their GO studies were performed to analyze their functions. The gene network was established and the pathways through which these DEGs were deregulated were also identified. The study provides a new platform for the determination of pathogenesis of colorectal cancer. The differential analysis revealed 7 differentially expressed signature genes out of 50 DEGs on the basis of physicochemical and functional analysis (p < 0.05) that showed involvement in the progression of colorectal cancer. These signature genes are CALD1, CTNNB1, CXCL14, PTCH1, CXCL8, TNFAIP3, and NNMT. The functional role of these genes in colorectal cancer and their dysregulation has been extensively studied [27][28][29][30]. Out of seven genes, two genes were upregulated while the rest showed downregulation. The GO study revealed that following functional categories were enriched among dysregulated genes; response to molecule of bacterial origin, response to a drug, cellular response to lipopolysaccharide, chemotaxis, movement of a cell or subcellular component and branching involved in ureteric bud morphogenesis. These genes showed a link to important biological pathways such as, methylation, beta-catenin signaling cascade and wnt canonical pathway. The dysregulation of these genes can cause Pilomatrixoma, congenital lung cyst, and other clinical phenotypes.

The network study showed the functional association of possible biomarker candidates with other interacting protein targets such as APC, AXIN, MAPK, TRAF, GLI, and SHH. The mutation of APC genes has been shown to be present in 90% of the patients with human CRC that interacts with CTNNB1 in the Wnt pathway. More than 80 target genes showed a connection with the source genes in causing colorectal cancer. The mutation of Kras genes also plays a pivotal role in the progression of colorectal cancer during the early adenoma stage. The cross talk between the wnt/β-catenin and RAS-ERK pathway exist and the interaction between the two pathways during the various stages of colorectal cancer the combined mutations of which lead to malignant transformation of CRC [31]. The interaction between the NNMT and the MAP/ERK pathway has also been under investigation reporting the cell survival, apoptosis and cell cycle progression of cancer tissues. The overexpression of NNMT has indicated the acceleration of cell proliferation by regulating the energy metabolism in CRC tissues and by its involvement with the P13K/Akt and MAP/ERK pathways [27]. The GLi and SHH are part of the hedgehog signaling pathway that plays an essential role in the differentiation, growth, tissue patterning and cell maintenance of various cancers. However, its role in the CRC is still controversial [32]. PTCH1 is a tumor suppressor gene and its downregulation causes the activation of GLi transcription factors that activate the hedgehog target genes. CXCL14 is another potential tumor inhibiting gene in colorectal carcinoma and downregulation of this gene may result in a more aggressive phenotype of colorectal cancer [30]. Another prognostic biomarker of colorectal cancer is the TNFAIP3 which may also act as the tumor suppressor gene [33]. The network analysis revealed that these biomarkers play an essential role in colorectal cancer and that the dysregulation of these genes may lead to the progression of cancer. Targeting these pathways and the genes involved in the signaling of these pathways may help in easing the therapeutic profiling of colorectal cancer. The CTNNB1 and NNMT are known targets of CRC and both genes are known to interact with the MAPK pathways in causing CRC. The integrated network-based analysis helped in identifying the interaction of these potential biomarkers with other target genes through different integrated pathways.

Conclusion

Advancement in the clinical therapy of diseases is still a requisite and to improve the diagnostic measures validated biomarkers can aid in the diagnosis. The microarray analysis has helped in several ways to identify the

Fig. 1 Fig. 2
12MA plots of an individual quality array after normalization. M and A is specified as M = log 2 (I 1 ) − log 2 (I 2 ), A = 1/2 log 2 (I 1 ) − log 2 (I 2 ) , where I 1 is the intensity of the array studied, and I 2 is the intensity of a "pseudo"-array that consists of the median across arrays". Normally, the mass of distribution in the MA plot is expected to be concentrated along the M = 0 axis with no trend in M as a function of A Ilyas et al. RNA degradation plot of each dataset produced by plot AffyRNAdeg showing 5′ to 3′ trend to evaluate the severity of RNA degradation and significance level

Fig. 3
3Cluster analysis of 7 colorectal related DEGs. Blue corresponds to a small distance and Red to a large distance. Lines indicate the boundaries of the clusters in the level of the tree

Fig. 4 aFig. 5
45Clinical phenotypes analysis of CRC related DEGs. b Biological pathway analysis using FunRich tool A genetic network of a total number of gene signatures associated with CRC differentially expressed seeder genes. Red nodes represent CRC seeder genes, blue nodes showing signature genes associated with seeder genes having no role in CRC while pink nodes represent gene signatures associated with seeder genes having a role inCRC Fig. 6Pathway modeling. Integrated genome to phenome scale signaling pathways involved in CRC. KEGG pathway was used to map the gene signatures for signaling and metabolic reconstruction

Fig. 7
7Interactive scatter plot indicates the expression-level of differentially expressed genes in colorectal cancer. These plots showed the consequence of RNA and protein levels on clinical survival

Table 1
1List of cDNA datasetsAccession No. Total samples Tissues
Species
Conditions/
type

Platform
Size of arrays
AffyIDs References

GSE 9412
6
Colorectal
cancer

Homo sapiens Sensitive vs
resistant

GPL571 [HG-
U133A_2]
Affym-
etrix Human
Genome
U133A 2.0
Array

732x732 fea-
tures

22277
Selga et al. [34]

GSE 11440
6
Colon
Homo sapiens Sensitive vs
resistant

GPL570 [HG-
U133_Plus_2]
U133 Plus 2.0
Array

1164x1164
features

54675
Mencia et al. [35]

GSE14773
8
Colon
Homo sapiens Control vs
treated

GPL570 [HG-
U133_Plus_2]
U133 Plus 2.0
Array

1164x1164
features

54675
Hwang et al. [36]

GSE 15102
8
Colon
Homo sapiens Control vs
treated

GPL571 [HG-
U133A_2]
Affym-
etrix Human
Genome
U133A 2.0
Array

732x732 fea-
tures

22277
Sagiv et al. [37]

GSE 18560
12
Colorectal
Homo sapiens Control vs
treated

GPL570 [HG-
U133_Plus_2]
Affym-
etrix Human
Genome U133
Plus 2.0 Array

1164x1164
features

54675
Selga et al. [34]

GSE 27157
10
Colorectal
cancer

Homo sapiens p53 wild vs.
tumor sam-
ples

GPL570 [HG-
U133_Plus_2]
Affym-
etrix Human
Genome U133
Plus 2.0 Array

1164x1164
features

54675
Katkoori et al.
[38]

GSE 29316
6
Colon fibroblast Homo sapiens Control vs
treated

GPL570 [HG-
U133_Plus_2]
Affym-
etrix Human
Genome U133
Plus 2.0 Array

1164x1164
features

54675
Chen et al. [39]

GSE 32323
44
Colorectal
cancer

Homo sapiens Control vs
Treated

GPL570 [HG-
U133_Plus_2]
Affym-
etrix Human
Genome U133
Plus 2.0 Array

1164x1164
features

54675
Khamas et al. [40]

GSE 35144
64
Colorect cancer Homo sapiens Case vs control GPL570 [HG-
U133_Plus_2]
Affym-
etrix Human
Genome U133
Plus 2.0 Array

1164x1164
features

54675
Uronis et al. [41]

GSE 55624
18
Colorectal
cancer

Homo sapiens Control vs
treated

GPL570 [HG-
U133_Plus_2]
Affym-
etrix Human
Genome U133
Plus 2.0 Array

1164x1164
features

54675
Schoumacher
et al. [42]

Table 2
2The differentially expressed CRC-associated genes curated from PubMedS.NO. Probe ID
Gene ID Uniprot_ID
PubMed Count Protein name
Reference links

1.
202237_at
NNMT
NNMT_HUMAN
4
NNMT Homo sapiens nicotinamide
N-methyltransferase

https ://www.ncbi.nlm.nih.gov/
pubme d/?term=%22NNM
T%22+AND+%22COL ORECT
AL+CANCE R%22

2.
212077_at
CALD1
CALD1_HUMAN
5
Caldesmon 1
https ://www.ncbi.
nlm.nih.gov/pubme
d/?term=%22+CALD1
%22+AND+%22COL ORECT
AL+CANCE R%22

3.
201533_at
CTNNB1
CTNB1_HUMAN 506
CTNNB1 Homo sapiens catenin beta 1 https ://www.ncbi.
nlm.nih.gov/pubme
d/?term=%22+CTNNB
1%22+AND+%22COL ORECT
AL+CANCE R%22

4.
222484_s_at
CXCL14
CXL14_HUMAN
3
C-X-C motif chemokine ligand 14
https ://www.ncbi.
nlm.nih.gov/pubme
d/?term=%22+CXCL1
4+%22+AND+%22COL
ORECT AL+CANCE R%22

5.
209815_at
PTCH1
PTC1_HUMAN
15
Patched 1
https ://www.ncbi.
nlm.nih.gov/pubme
d/?term=%22+PTCH1
+%22+AND+%22COL
ORECT AL+CANCE R%22

6.
202644_s_at
TNFAIP3
TNAP3_HUMAN
26
TNF alpha induced protein 3
https ://www.ncbi.nlm.nih.gov/
pubme d/?term=%22+TNFAI
P3%22+AND+%22COL
ORECT AL+CANCE R%22

7.
202859_x_at CXCL8
5
C-X-C motif chemokine ligand 8
https ://www.ncbi.
nlm.nih.gov/pubme
d/?term=%22+CXCL8
+%22+AND+%22COL
ORECT AL+CANCE R%22

AcknowledgementsNot applicable.Page 12 of 13Ilyas et al. J of Biol Res-Thessaloniki (2020)27:8novel targets for targeted based therapies. This study reveals the essential biomarkers involved in CRC through a system biology approach. Seven essential biomarkers of CRC having functional relation with other important target proteins such as APC, MAPK and GLi and have found a significant association with CRC. The study might help in rapid risk assessment of colorectal cancer by providing the new insights in clinical practice utilizing the microarray gene expression analysis.Supplementary informationSupplementary information accompanies this paper at https ://doi. org/10.1186/s4070 9-020-00118 -1.Additional file 1:Table S1. The function summaryAffyRNAdeg of Bioconductor package produced a single summary-statistic for each array in the batch dataset.Additional file 2:Table S2. List of databases, software, and tools used in this study.Additional file 3:Table S3. Preliminary investigation of common and related differentially expressed genes of each microarray dataset.Authors' contributions SA and SZ conceived and designed the study. RA and UI carried out the research work. HN and SZ provided guidance with study design. All authors contributed in manuscript writing and edition. HN and SA read and approved the final manuscript. All authors read and approved the final manuscript.FundingNot applicable.Availability of data and materialsThe data has been presented with the article.Ethics approval and consent to participateNot applicable.Consent of publicationNot applicable.Competing interests
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