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Uploading README and two datasets. One is progressing and the other one is non-progressing

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  1. README.md +156 -3
  2. non_progressing_subset.csv +65 -0
  3. progressing_subset.csv +65 -0
README.md CHANGED
@@ -1,3 +1,156 @@
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- ---
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- license: mit
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- ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ # DNA Methylation Analysis Dataset
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+
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+ ## Executive Summary
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+ DNA methylation plays a vital role in the regulation of gene expression and is implicated in cancer progression. This dataset and analysis focus on comparing methylation profiles between non-invasive and invasive breast cancer subtypes, with the goal of identifying epigenetic markers for early detection and therapeutic intervention.
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+
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+ ### Motivation
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+ - Improve understanding of epigenetic changes driving the transition from non-invasive to invasive breast cancer.
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+ - Aid in the development of diagnostic and prognostic tools for personalized cancer treatment.
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+
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+ ### Potential Applications
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+ - Biomarker discovery for early detection.
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+ - Epigenetic therapeutic target identification.
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+ - Advancement of precision oncology through methylation-based profiling.
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+
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+ ---
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+
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+ ## Description of Data
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+ This dataset contains DNA methylation beta values (the ratio of methylated to unmethylated CpG sites) derived from patient samples categorized into two subsets:
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+
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+ Non-Progressing Subset:
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+ File: non_progressing_subset.csv
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+
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+ Contains methylation beta values for CpG sites in samples classified as non-progressing (e.g., patients with non-invasive cases).
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+ Includes metadata such as sample IDs, group labels.
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+
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+ Progressing Subset:
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+ File: progressing_subset.csv
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+
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+ Contains methylation beta values for CpG sites in samples classified as progressing (e.g., patients with advancing conditions or invasive cases).
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+
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+ ---
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+
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+ ## Data Collection
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+
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+ The dataset was curated from the following sources:
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+
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+ NCBI DNA Methylation Database: Publicly available DNA methylation data was downloaded from the National Center for Biotechnology Information (NCBI).
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+
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+ Web Scraping Tool: A custom web scraping tool was developed to gather additional sample metadata from relevant online sources. The tool scraps patient information and maps the metadata back to the DNA methylation data, enabling a more comprehensive analysis.
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+
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+ The scripts for data scraping and mapping are included in this repository under the file webScrappingProcessing.py.
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+
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+ ---
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+
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+ ## Power Analysis
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+ A power analysis was conducted to determine the minimum sample size required to detect significant methylation differences between groups:
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+ - **Effect Size**: Medium (Cohen’s d = 0.5).
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+ - **Significance Level (α)**: 0.05.
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+ - **Power (1-β)**: 0.8.
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+
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+ The required sample size per group was calculated using the TTestIndPower module from statsmodels.
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+
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+ Required sample size per group: 63.77
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+
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+ The results confirmed that the dataset size is sufficient to detect biologically meaningful differences in methylation levels with statistical confidence.
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+
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+ ---
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+
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+ ## Exploratory Data Analysis (EDA)
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+
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+ Exploratory data analysis revealed key insights into the methylation profiles:
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+
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+ the CpG sites associated with the genes PRAC2, TDRD10, and TMEM132C have been highlighted for their diagnostic and prognostic relevance in breast cancer. Specifically, the CpG sites cg12374721 (PRAC2), cg18081940 (TDRD10), and cg04475027 (TMEM132C) have shown promise as biomarkers.
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+ Reference: https://rdcu.be/d1vq6
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+
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+ Statistical Comparison: Key CpG sites were analyzed, including cg12374721, cg18081940, and cg04475027.
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+
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+
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+ For each CpG site, the mean and variance of methylation levels were calculated for progressing and non-progressing samples.
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+
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+ Box Plots:
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+ The box plots below compare the methylation levels of progressing and non-progressing samples for significant CpG sites:
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+
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+
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+ Comparison of cg12374721 between progressing and non-progressing samples
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+ ![Figure 1](Figure_1.png)
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+
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+
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+ Comparison of cg18081940 between progressing and non-progressing samples
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+ ![Figure 1](Figure_2.png)
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+
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+ Comparison of cg04475027 between progressing and non-progressing samples
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+ ![Figure 1](Figure_3.png)
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+
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+ Statistical Results:
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+ Summary statistics and p-values for the differential methylation analysis are included in the file cpg_sites_statistical_results.csv.
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+
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+ | **CpG Site** | **T-Statistic** | **P-Value** |
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+ |----------------|-----------------------|------------------------|
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+ | cg12374721 | -1.3929 | 0.1661 |
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+ | cg18081940 | -1.6760 | 0.0962 |
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+ | cg04475027 | -0.1902 | 0.8494 |
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+
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+ Observations:
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+ CpG site cg18081940 shows the most promising difference between progressing and non-progressing groups, with a p-value close to the threshold for significance (p = 0.0962).
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+ Other CpG sites (cg12374721 and cg04475027) did not show statistically significant differences at α = 0.05.
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+
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+ Code for EDA: The analysis code is included in the repository as eda.py.
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+
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+ ---
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+
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+ ## Data Sourcing Code
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+ The data sourcing and processing code are publicly available in the following repository:
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+ [\[**Public Data Sourcing Code Repository**\].](https://github.com/kz110AIPI/aipi510Project.git)
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+
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+ This repository contains:
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+ - Scripts for raw data acquisition from public databases.
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+ - Pipelines for data preprocessing, normalization, and feature extraction.
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+
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+ ## Please run code with this order:
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+
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+ 1. webScrappingProcessing.py
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+ 2. ncbiDataProcessing.py
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+ 3. dataMerging.py
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+ 4. subsetting.py
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+ 5. eda.py
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+
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+ ---
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+
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+ ## Ethics Statement
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+ This project complies with strict ethical standards to ensure the responsible use of biomedical data:
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+ - **Privacy**: All patient data is anonymized in accordance with HIPAA and GDPR requirements.
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+ - **Consent**: Datasets originate from studies with proper informed consent protocols.
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+ - **Bias Mitigation**: Efforts were made to ensure representation across diverse populations.
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+ - **Research Integrity**: Findings are intended for academic research and not direct clinical application.
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+
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+ ---
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+
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+ ## License
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+ This dataset and code are licensed under the **MIT License**.
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+
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+ MIT License
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+
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+ Copyright (c) 2024 Kai
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
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+
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+
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+ ---
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+
non_progressing_subset.csv ADDED
@@ -0,0 +1,65 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ id_ref,cg18081940,cg04475027,cg12374721,case_control
2
+ meth.sample.141,0.546885829048798,0.579566695749592,0.563957852211146,Non-progressor
3
+ meth.sample.141.detectionpval,0.0,0.0,0.0,Non-progressor
4
+ meth.sample.143,0.127020754520792,0.743414198902315,0.256854880606835,Non-progressor
5
+ meth.sample.143.detectionpval,0.0,0.0,1.23792951252102e-13,Non-progressor
6
+ meth.sample.58,0.565249445983423,0.676427490381524,0.631187303787722,Non-progressor
7
+ meth.sample.58.detectionpval,1.30969595823682e-81,2.44818409774158e-77,1.56255378753126e-87,Non-progressor
8
+ meth.sample.117,0.118022880241546,0.553022479416511,0.190478948671225,Non-progressor
9
+ meth.sample.117.detectionpval,0.0,0.0,1.74853740432832e-233,Non-progressor
10
+ meth.sample.78,0.119605301180971,0.28736037030087,0.367319243972082,Non-progressor
11
+ meth.sample.78.detectionpval,4.8727781163005995e-129,6.718391184268211e-17,6.38470409357228e-137,Non-progressor
12
+ meth.sample.167,0.164819808383778,0.289910984405543,0.389300564745278,Non-progressor
13
+ meth.sample.167.detectionpval,3.07548633207481e-59,4.71299973207749e-17,2.731209215619619e-92,Non-progressor
14
+ meth.sample.124,0.0228103962723076,0.121254585318109,0.5347557475658,Non-progressor
15
+ meth.sample.124.detectionpval,0.0,1.0756658023984799e-36,3.011396190466749e-232,Non-progressor
16
+ meth.sample.185,0.58317829780768,0.564641034229256,0.375692692484545,Non-progressor
17
+ meth.sample.185.detectionpval,0.0,0.0,1.2132233044795898e-258,Non-progressor
18
+ meth.sample.93,0.177194147530052,0.309180347181396,0.254069075421992,Non-progressor
19
+ meth.sample.93.detectionpval,0.0,0.0,0.0,Non-progressor
20
+ meth.sample.126,0.435743462739608,0.678130227432384,0.139993832266311,Non-progressor
21
+ meth.sample.126.detectionpval,0.0,0.0,0.0,Non-progressor
22
+ meth.sample.45,0.687298863685237,0.49752444453637,0.5817918376772,Non-progressor
23
+ meth.sample.45.detectionpval,0.0,0.0,1.3601029255838501e-203,Non-progressor
24
+ meth.sample.160,0.148204659565971,0.21916995522757,0.091826724812856,Non-progressor
25
+ meth.sample.160.detectionpval,0.0,0.0,0.0,Non-progressor
26
+ meth.sample.128,0.265204406206508,0.0652045468516642,0.132616783791813,Non-progressor
27
+ meth.sample.128.detectionpval,0.0,3.063558871261731e-245,4.4858387019879397e-228,Non-progressor
28
+ meth.sample.36,0.344270721658888,0.668428881505074,0.278485814292061,Non-progressor
29
+ meth.sample.36.detectionpval,0.0,0.0,1.38267570334533e-199,Non-progressor
30
+ meth.sample.188,0.615470616711705,0.578733957628101,0.527388854870206,Non-progressor
31
+ meth.sample.188.detectionpval,0.0,1.31432357346632e-296,3.7403269736567e-68,Non-progressor
32
+ meth.sample.104,0.709676460160479,0.615525086228014,0.615905249046667,Non-progressor
33
+ meth.sample.104.detectionpval,0.0,2.72040681191063e-273,0.0,Non-progressor
34
+ meth.sample.115,0.342901626111537,0.268593901942888,0.453194104127109,Non-progressor
35
+ meth.sample.115.detectionpval,0.0,1.4477684497195101e-167,5.9933631251777986e-208,Non-progressor
36
+ meth.sample.130,0.443261228247137,0.245716396911934,0.238513529644204,Non-progressor
37
+ meth.sample.130.detectionpval,0.0,6.55537709987994e-218,3.81558381212378e-166,Non-progressor
38
+ meth.sample.191,0.158886117912515,0.0864789582389941,0.262858470319301,Non-progressor
39
+ meth.sample.191.detectionpval,0.0,0.0,2.23303238505918e-280,Non-progressor
40
+ meth.sample.38,0.435635104512466,0.67812249199223,0.142098701082218,Non-progressor
41
+ meth.sample.38.detectionpval,3.19060133471114e-241,7.96159385282492e-136,7.57368754260938e-72,Non-progressor
42
+ meth.sample.190,0.0633572150370354,0.701744553881607,0.173097509795993,Non-progressor
43
+ meth.sample.190.detectionpval,0.0,0.0,1.1320460527662099e-124,Non-progressor
44
+ meth.sample.31,0.394747684010791,0.280799557349948,0.359496517920463,Non-progressor
45
+ meth.sample.31.detectionpval,0.0,0.0,1.0551746800034499e-252,Non-progressor
46
+ meth.sample.138,0.086026736545922,0.189844326248598,0.197239814968688,Non-progressor
47
+ meth.sample.138.detectionpval,0.0,2.24571412630639e-109,1.51050351142462e-122,Non-progressor
48
+ meth.sample.134,0.389077197233155,0.404075248708632,0.463461223839232,Non-progressor
49
+ meth.sample.134.detectionpval,5.97707285610494e-31,6.97891117885879e-21,3.8702555675982594e-12,Non-progressor
50
+ meth.sample.110,0.480118694203682,0.561847483671053,0.200344411823855,Non-progressor
51
+ meth.sample.110.detectionpval,0.0,0.0,2.1145046243548305e-259,Non-progressor
52
+ meth.sample.60,0.210808618672799,0.388473728082857,0.558736862610764,Non-progressor
53
+ meth.sample.60.detectionpval,0.0,1.0549561395291e-222,3.141929332445841e-198,Non-progressor
54
+ meth.sample.187,0.441932328845191,0.341775132225477,0.19420235649616,Non-progressor
55
+ meth.sample.187.detectionpval,0.0,1.48857379358855e-231,0.0,Non-progressor
56
+ meth.sample.146,0.287138762476892,0.0487727852931143,0.154065155197486,Non-progressor
57
+ meth.sample.146.detectionpval,0.0,0.0,0.0,Non-progressor
58
+ meth.sample.189,0.451737693025796,0.626283799990037,0.26300552499006,Non-progressor
59
+ meth.sample.189.detectionpval,0.0,5.21069915523596e-136,1.01255459470411e-88,Non-progressor
60
+ meth.sample.150,0.232310830243621,0.0973497339615716,0.328281094039718,Non-progressor
61
+ meth.sample.150.detectionpval,4.23142491081849e-164,3.6184663309607397e-246,2.01723592459292e-30,Non-progressor
62
+ meth.sample.65,0.040887954770387,0.467738950981545,0.508067080146482,Non-progressor
63
+ meth.sample.65.detectionpval,0.0,1.49214016644298e-186,9.43622684209039e-99,Non-progressor
64
+ meth.sample.176,0.113084287277131,0.0740212182339135,0.185411759746444,Non-progressor
65
+ meth.sample.176.detectionpval,0.0,0.0,5.1353992711588406e-235,Non-progressor
progressing_subset.csv ADDED
@@ -0,0 +1,65 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ id_ref,cg18081940,cg04475027,cg12374721,case_control
2
+ meth.sample.140,0.625380965451227,0.540178547129978,0.45168982174025,Progressor
3
+ meth.sample.140.detectionpval,0.0,1.6025483379259603e-188,0.0,Progressor
4
+ meth.sample.139,0.216403191645357,0.491761325107203,0.3847466863176,Progressor
5
+ meth.sample.139.detectionpval,0.0,0.0,0.0,Progressor
6
+ meth.sample.142,0.662640585020811,0.155252702208767,0.478766586372817,Progressor
7
+ meth.sample.142.detectionpval,0.0,1.5515821057287e-116,0.0,Progressor
8
+ meth.sample.151,0.083346480429898,0.200434208876396,0.137105203277455,Progressor
9
+ meth.sample.151.detectionpval,0.0,4.30290671317062e-103,6.787497048380079e-168,Progressor
10
+ meth.sample.157,0.120663603474197,0.40894449031775,0.257361775695919,Progressor
11
+ meth.sample.157.detectionpval,1.53178960352287e-76,2.5996074741739197e-49,4.26262274208701e-64,Progressor
12
+ meth.sample.64,0.492769423266931,0.631899156080669,0.505763056625892,Progressor
13
+ meth.sample.64.detectionpval,9.15041571643391e-197,1.0853114760128399e-49,1.00673973239353e-153,Progressor
14
+ meth.sample.28,0.462993961329297,0.30443007553639,0.0742811015065959,Progressor
15
+ meth.sample.28.detectionpval,0.0,1.3060898263609e-220,0.0,Progressor
16
+ meth.sample.108,0.714664169987344,0.681190901677844,0.518006048526545,Progressor
17
+ meth.sample.108.detectionpval,0.0,7.0472648633033e-72,1.24106943961159e-100,Progressor
18
+ meth.sample.75,0.734828314254025,0.260587321609789,0.658598970322053,Progressor
19
+ meth.sample.75.detectionpval,0.0,0.0,0.0,Progressor
20
+ meth.sample.12,0.437033213318966,0.363347281242136,0.503507063665497,Progressor
21
+ meth.sample.12.detectionpval,0.0,0.0,0.0,Progressor
22
+ meth.sample.129,0.611925860265959,0.610098077488738,0.598589153223636,Progressor
23
+ meth.sample.129.detectionpval,0.0,0.0,0.0,Progressor
24
+ meth.sample.111,0.293800450853041,0.623419658604922,0.107708709065709,Progressor
25
+ meth.sample.111.detectionpval,0.0,0.0,1.67324502871373e-264,Progressor
26
+ meth.sample.41,0.636621494466368,0.471970155140373,0.317526854084774,Progressor
27
+ meth.sample.41.detectionpval,0.0,3.1738074583626096e-48,4.633750551293131e-117,Progressor
28
+ meth.sample.163,0.362179169493935,0.468670325439145,0.761114081016236,Progressor
29
+ meth.sample.163.detectionpval,0.0,0.0,0.0,Progressor
30
+ meth.sample.23,0.401972171199662,0.188088731455473,0.411597119282498,Progressor
31
+ meth.sample.23.detectionpval,0.0,0.0,0.0,Progressor
32
+ meth.sample.171,0.0678855653548266,0.0972170721428093,0.33834246056229,Progressor
33
+ meth.sample.171.detectionpval,0.0,0.0,4.29910549532837e-255,Progressor
34
+ meth.sample.127,0.523150418970575,0.318435181118678,0.36714506174446,Progressor
35
+ meth.sample.127.detectionpval,0.0,0.0,6.63346138656676e-125,Progressor
36
+ meth.sample.47,0.27871382511648,0.367624071730812,0.471565265902669,Progressor
37
+ meth.sample.47.detectionpval,0.0,2.3911694686567602e-111,9.86106998135443e-178,Progressor
38
+ meth.sample.89,0.685901848406162,0.89789806141576,0.870489925796375,Progressor
39
+ meth.sample.89.detectionpval,0.0,0.0,0.0,Progressor
40
+ meth.sample.42,0.093991492721117,0.158292686028518,0.173502835232262,Progressor
41
+ meth.sample.42.detectionpval,0.0,7.99368398261012e-176,0.0,Progressor
42
+ meth.sample.61,0.831957646438177,0.777080404934191,0.886548560285419,Progressor
43
+ meth.sample.61.detectionpval,0.0,2.71753095137889e-121,0.0,Progressor
44
+ meth.sample.6,0.553350103193852,0.433301870814486,0.500669738672678,Progressor
45
+ meth.sample.6.detectionpval,0.0,0.0,0.0,Progressor
46
+ meth.sample.96,0.473438821263929,0.643613137529778,0.395407378562965,Progressor
47
+ meth.sample.96.detectionpval,0.0,0.0,0.0,Progressor
48
+ meth.sample.168,0.413046215227235,0.250099471694669,0.320023725084169,Progressor
49
+ meth.sample.168.detectionpval,0.0,0.0,0.0,Progressor
50
+ meth.sample.125,0.807567110771747,0.563725990048744,0.655536292871028,Progressor
51
+ meth.sample.125.detectionpval,0.0,0.0,1.81529558650427e-263,Progressor
52
+ meth.sample.16,0.642521623778111,0.575706618268426,0.1593589926181,Progressor
53
+ meth.sample.16.detectionpval,0.0,0.0,0.0,Progressor
54
+ meth.sample.9,0.353654795450365,0.207251940521467,0.523275561385135,Progressor
55
+ meth.sample.9.detectionpval,0.0,0.0,0.0,Progressor
56
+ meth.sample.68,0.428091905925954,0.430627950693436,0.359394332619176,Progressor
57
+ meth.sample.68.detectionpval,1.60065613843431e-228,2.831565302851909e-34,2.90463448349433e-88,Progressor
58
+ meth.sample.20,0.325096089674983,0.0987275129001546,0.529230828233381,Progressor
59
+ meth.sample.20.detectionpval,6.89682972525937e-108,1.3044797531021e-138,1.08742613810522e-142,Progressor
60
+ meth.sample.43,0.404135590445898,0.243616175600432,0.428907374244072,Progressor
61
+ meth.sample.43.detectionpval,0.0,1.1904346869208195e-114,1.81910562022412e-160,Progressor
62
+ meth.sample.186,0.378197277883608,0.327444480517551,0.463791241711827,Progressor
63
+ meth.sample.186.detectionpval,0.0,0.0,0.0,Progressor
64
+ meth.sample.35,0.802283744563387,0.67144020070957,0.757308990186301,Progressor
65
+ meth.sample.35.detectionpval,0.0,0.0,0.0,Progressor