Title of Invention: HIGH THROUGHPUT DETECTION OF MICRORNAS AND USE FOR DISEASE DIAGNOSIS Abstract: Methods, compositions and kits are provided for high throughput detection of micro RNAs (miRNA), especially for sensitive and specific detection of miRNA that are in low abundance and closely related to each other. In particular, an assembly of designed oligonucleotide probes with unique tag sequences is used to achieve these purposes via high throughput microarrays, optionally in conjunction with branched-DNA based array detection. The assays can be used for diagnosis, prognosis or monitoring of diseases or disorders such as cancer, for pharmacogenomic studies of patient stratification and drug responses, for discovery of therapeutic targets, or for forensic analysis. Detailed Description: CROSS-REFERENCE This application claims the benefit of U.S. Provisional Application No. 61/020,693, filed Jan. 11, 2008, which application is incorporated herein by reference in its entirety. BACKGROUND OF THE INVENTION Nucleic acid analysis is becoming an important tool for the diagnosis and prognosis of infectious as well as genetic diseases. For instance, new discovered microRNAs (miRNAs) are important to the regulation of gene expression. These small molecules inhibit protein production through selective binding to the complementary messenger RNA sequences. Although the inhibition-mediated biological function of these miRNA molecules are not yet fully understood, miRNAs seems to be crucial in diverse regulations, including development, cell differentiation, proliferation, apoptosis, and maintenance of stemness and imprinting. Moreover, for an increasing number of genetic diseases, the genes involved have been identified and mutant alleles characterized. Large-scale multiplex analysis of nucleic acid is needed for practical identification of individuals, e.g., for paternity testing and in forensic science, for organ-transplant donor-recipient matching, for genetic disease diagnosis, prognosis, and pre-natal counseling, and the study of oncogenic mutations. In addition, the cost-effectiveness of infectious disease diagnosis by nucleic acid analysis varies directly with the multiplex scale in panel testing. Many of these applications depend on the discrimination of single-base differences at a multiplicity of sometimes closely spaced loci. Although there are many techniques currently used to detect target nucleic acids, the need remains for a rapid single assay format to detect the presence or absence of multiple selected sequences in a polynucleotide sample. SUMMARY OF THE INVENTION The invention relates to methods, compositions and devices, e.g., for detecting a target nucleic acid in a sample. In one aspect, the invention provides a method for detecting a target nucleic acid in a sample. In some embodiments of this aspect, the invention provides an oligonucleotide probe set. In some embodiments, the invention provides at least one oligonucleotide probe set, each set containing (i) a first oligonucleotide probe having a 5′ target specific region and a first 3′ universal sequence region, (ii) a second oligonucleotide probe having a 3′ target specific region and a second 5′ universal sequence region, (iii) a third oligonucleotide probe having a 5′ region complementary to the first 3′ universal sequence region in the first probe, and (v) a fourth oligonucleotide probe having a 3′ region complementary to the 5′ universal sequence region of the second oligonucleotide probe. In some embodiments, the first and the second oligonucleotides probes are suitable for ligation together when hybridized adjacent to one another to the target nucleic acid. In some embodiments, the third and the fourth oligonucleotides probes are suitable for ligation to the target nucleic acid when hybridized adjacent to the nucleic acid target. The oligonucleotide probe set is annealed to the target nucleic acid such that a complex is formed between the target nucleic acid and the oligonucleotide probe set, and the complex is contacted with a linking agent under conditions such that the directly adjacent 5′ and 3′ ends of the first and second oligonucleotide probes, the 3′ and 5′ ends of the third oligonucleotide probe and the target nucleic acid, and the 5′ and 3′ ends of the fourth oligonucleotide probe and the target nucleic acid covalently bond to form a ligated probe product. The ligated probe product is separated from the non-ligated first and second oligonucleotide probes, and the ligated probe product is detected, where the presence of the ligated product is indicative of presence of a target nucleic acid in the sample. In some embodiments, the probes in the oligonucleotide probe set have a predetermined sequence. In some embodiments, the first oligonucleotide probe contains in a 3′ to 5′ order a universal region, a tag region and a target specific region. In some embodiments, the second oligonucleotide probe contains in a 3′ to 5′ order a target specific region, a tag region and a universal sequence region. In some embodiments, the third oligonucleotide probe contains a 3′ region that is complementary to the tag region of the first oligonucleotide probe. In some embodiments of the methods, the invention provides a fifth oligonucleotide probe that is complementary to the tag region of the first oligonucleotide probe. In some embodiments, the fourth oligonucleotide probe contains 5′ region that is complementary to the tag region of the second oligonucleotide probe. In some embodiments of the methods, the invention provides a sixth oligonucleotide probe that is complementary to the tag region of the second oligonucleotide probe. In some embodiments, the tag region in the first oligonucleotide probe or the tag in the second oligonucleotide probe are specifically assigned to the target nucleic acid. In some embodiments, at least one of the universal regions of the first and the second oligonucleotide probe is a promoter sequence. The promoter sequence can be used as a primer of DNA polymerase. Examples of DNA polymerase include, but are not limited to, Thermoanaerobacter thermohydrosulfuricus DNA polymerase, Thermococcus litoralis DNA polymerase I, E. coli DNA polymerase I, Taq DNA polymerase I, Tth DNA polymerase I, Bacillus stearothermophilus (Bst) DNA polymerase I, E. coli DNA polymerase III, bacteriophage T5 DNA polymerase, bacteriophage M2 DNA polymerase, bacteriophage T4 DNA polymerase, bacteriophage T7 DNA polymerase, bacteriophage phi29 DNA polymerase, bacteriophage PRD1 DNA polymerase, bacteriophage phi15 DNA polymerase, bacteriophage phi21DNA polymerase, bacteriophage PZE DNA polymerase, bacteriophage PZA DNA polymerase, bacteriophage Nf DNA polymerase, bacteriophage M2Y DNA polymerase, bacteriophage B103 DNA polymerase, bacteriophage SF5 DNA polymerase, bacteriophage GA-1 DNA polymerase, bacteriophage Cp-5 DNA polymerase, bacteriophage Cp-7 DNA polymerase, bacteriophage PR4 DNA polymerase, bacteriophage PR5 DNA polymerase, bacteriophage PR722 DNA polymerase and bacteriophage L17 DNA polymerase. In some embodiments, the promoter sequence is a promoter for a phage polymerase. Examples of phage polymerase include, but are not limited to, T7 RNA polymerase, T3 RNA polymerase or SP6 RNA polymerase. In some embodiments of the methods, the invention includes annealing a first primer complementary to the universal sequence region of the first oligonucleotide probe, and contacting the annealed primer with a polymerase under conditions such that the annealed primer is extended to form an extension product complementary to the sequences to which the primers is annealed. In some embodiments, the presence of the extension product is detected, where the presence of the extended product is indicative of the presence of the target nucleic acid in the sample. In some embodiments of the methods, the invention includes annealing a second primer complementary to the universal sequence region of the fourth oligonucleotide probe, and contacting the annealed second primer with a polymerase under conditions such that the annealed primer is extended to form an extension product complementary to the sequences to which the primers is annealed. In some embodiments, the presence of the extension product is detected, where the presence of the extended product is indicative of the presence of the target nucleic acid in the sample. In some embodiments of the methods, the invention includes annealing a first primer complementary to the universal sequence region of the fourth oligonucleotide probe, contacting the annealed primer with a polymerase under conditions such that the annealed primer is extended to form extension products complementary to the sequences to which the primers is annealed. In some embodiments, the presence of the extension product is detected, where the presence of the extended product is indicative of the presence of the target nucleic acid in the sample. The extension products can be detected using a DNA microarray, bead microarray, high throughput sequencing or single microtiter plate assay. In some embodiments, the extension product has a detectable label. The detectable label can be a fluorescent or biotin label. In some embodiments, the invention includes detecting a fluorescent signal generated by the fluorescent, chemiluminescent or color. In some embodiments, the label is attached to the primer complementary to the universal sequence region of the first oligonucleotide probe. In some embodiments, the label is incorporated during the extension of the annealed primer complementary to the universal sequence region of the first oligonucleotide probe. In some embodiments, the incorporation includes adding a label nucleotide to the extension of the annealed primer complementary to the universal sequence region of the third oligonucleotide probe. In some embodiments, the universal sequence region of the second oligonucleotide is a phage promoter. Examples of phage promoters include, but are not limited to, T7 RNA polymerase promoter, T3 RNA polymerase promoter or SP6 RNA polymerase promoter. In some embodiments, the phage promoter is a T7 RNA polymerase promoter. In some embodiments of the methods, the invention includes contacting the phage promoter region of the second oligonucleotide probe with a phage polymerase under conditions such that a transcription product of the phage promoter region is formed and detecting the presence of the transcription product, where the presence of the transcription product is indicative of the presence of the target nucleic acid in the sample. In some embodiments, the transcription product is detected using a DNA microarray, bead microarray, high throughput sequencing or a single microtiter plate assay. In some embodiments, the transcription product has a detectable label. The detectable label can be a fluorescent or biotin label. In some embodiments, the invention includes detecting a fluorescent signal generated by the fluorescent or chemiluminescent or color. In some embodiments the label is incorporated during the transcription of the phage promoter region of the second oligonucleotide probe. In some embodiments, the incorporation includes adding a label nucleotide to the transcription of the phage promoter region of the second oligonucleotide probe. In some embodiments, the target nucleic acid is a miRNA molecule. In some embodiments, the miRNA molecule is derived from total RNA. In some embodiments, the first or third oligonucleotide contains a capturing portion. The capturing portion can be used to separate the ligated probe product from unligated first and second oligonucleotide probes. Examples of capturing portions include, but are not limited to, biotin and a capture sequence. In some embodiments, the capturing portion is biotin. In some embodiments, the ligated probe product is isolated by binding the biotin with a strepavidin bound to a solid support. In some embodiments of the methods, the invention provides a loop that links the second and the fourth oligonucleotide. In some embodiments, the invention includes detecting the presence of a ligated probe containing a loop to indicate the presence of the target nucleic acid in said sample. In some embodiments, detecting the presence of a ligated probe containing a loop includes binding a branched DNA to the ligated probe. In some embodiments, the ligated probe containing a loop is detected using a DNA microarray, bead microarray, or high throughput sequencing. INCORPORATION BY REFERENCE All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. BRIEF DESCRIPTION OF THE DRAWINGS The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which: FIG. 1 schematically illustrates an embodiment of the invention of miRNA annealing with two stacking oligos to form a miRNA/DNA hybrid FIG. 2: schematically illustrates an embodiment of the invention of miRNA forming a complex with four oligos stacked together FIG. 3: schematically illustrates an embodiment of the invention for probe preparation of miRNA FIG. 4 schematically illustrates an embodiment of the invention for a hair pin after ligation of miRNA complex with four oligos stacked together. FIG. 5 schematically illustrates an embodiment of the invention for analysis of miRNA. FIG. 6 schematically illustrates an embodiment of the invention for bDNA detection in a miRNA array assay FIG. 7 schematically illustrates an embodiment of the invention for probe preparation for bDNA detection using a complex with four oligos stacked together with the target nucleic acid FIG. 8 schematically illustrates an embodiment of the invention for analysis of miRNA. FIG. 9 shows the sequences for Let-7a, Let-7b and Let-7c miRNA in A, and shows discrimination of let 7 miRNA with a microarray in B. FIG. 10 shows an array profiling miRNA expression in HeLa cells with T7 transcription and PCR amplification. DETAILED DESCRIPTION OF THE INVENTION Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs. All patents and publications referred to herein are incorporated by reference in their entirety. The assay of the present invention is particularly useful for analyzing nucleic acids (DNA or RNA). The methods described herein provide a sensitive assay for determining the presence or absence of a target nucleic acid, e.g., the presence of absence of a point mutation or a SNP in a target nucleic acid. In some embodiments, the method described herein use oligonucleotide probes which are complementary to two contiguous predetermined sequences of the test substance. If these probes anneal in a juxtaposed position, there is a reasonable certainty that the sequence being investigated is the relevant one. The annealed probes are then exposed to a linking agent which then ligates the adjacent ends of the probes if the nucleotides base pair at the target nucleotide position. Then, the presence or absence of ligation is determined by one of a number of techniques to be described below. The oligonucleotide probe sets can be in the form of any nucleotide such as ribonucleotides, deoxynucleotides, modified ribonucleotides, modified deoxyribonucleotides, peptide nucleotide analogues, modified peptide nucleotide analogues, modified phosphate-sugar-backbone oligonucleotides, nucleotide analogs, and mixtures thereof. In some embodiments, the oligonucleotide probe sets are in the form of deoxynucleotides. The linking agent could be a ligase. In some embodiments the ligase is T4 DNA ligase, using well known procedures (Maniatis, T. in Molecular Cloning, Cold Spring Harbor Laboratory (1982)). Other DNA ligases may also be used. T4 DNA ligase may also be used when the target nucleic acid is RNA (The Enzymes, Vol. 15 (1982) by Engler M. J. and Richardson C. C., p. 16-17. Methods in Enzymology, Vol. 68 (1979) Higgins N. P. and Cozzarelli N. R. p. 54-56). With regard to ligation, other ligases, such as those derived from thermophilic organisms may be used thus permitting ligation at higher temperatures allowing the use of longer probes (with increased specificity) which could be annealed and ligated simultaneously under the higher temperatures normally associated with annealing such probes. The ligation, however, need not be by an enzyme and, accordingly, the linking agent may be a chemical agent which will cause the probes to link unless there is a nucleotide base pair mismatching at the target nucleotide position. For simplicity, some embodiments of the invention will be described using T4 DNA ligase as the linking agent. This enzyme requires the presence of a phosphate group on the 5′ end that is to be joined to a 3′ OH group on a neighboring oligonucleotide. In some cases, the methods described herein involve performing one or more genetic analyses or detection steps on nucleic acids. In some embodiments target nucleic acids are from a sample obtained from an animal. Such animal can be a human or a domesticated animal such as a cow, chicken, pig, horse, rabbit, dog, cat, or goat. Samples derived from an animal, e.g., human, can include, for example whole blood, sweat, tears, ear flow, sputum, lymph, bone marrow suspension, lymph, urine, saliva, semen, vaginal flow, cerebrospinal fluid, brain fluid, ascites, milk, secretions of the respiratory, intestinal or genitourinary tracts fluid. In some embodiments the sample is a cell sample. Cell samples can be obtained from a variety of tissues depending on the age and condition of the animal. Cell samples can be obtained from peripheral blood using well known techniques. In fetal testing, a sample can be obtained by amniocentesis, chorionic villi sampling or by isolating fetal cells from the blood of a pregnant individual. Other sources of nucleic acids include blood, semen, buccal cells, or the like. Nucleic acids can be obtained from any tissue or organ by methods well known in the art. To obtain a blood sample, any technique known in the art may be used, e.g. a syringe or other vacuum suction device. A blood sample can be optionally pre-treated or processed prior to enrichment. Examples of pre-treatment steps include the addition of a reagent such as a stabilizer, a preservative, a fixant, a lysing reagent, a diluent, an anti-apoptotic reagent, an anti-coagulation reagent, an anti-thrombotic reagent, magnetic property regulating reagent, a buffering reagent, an osmolality regulating reagent, a pH regulating reagent, and/or a cross-linking reagent. When a blood sample is obtained, a preservative such an anti-coagulation agent and/or a stabilizer can be added to the sample prior to enrichment. This allows for extended time for analysis/detection. Thus, a sample, such as a blood sample, can be analyzed under any of the methods and systems herein within 1 week, 6 days, 5 days, 4 days, 3 days, 2 days, 1 day, 12 hrs, 6 hrs, 3 hrs, 2 hrs, or 1 hr from the time the sample is obtained. In some embodiments, a blood sample can be combined with an agent that selectively lyses one or more cells or components in a blood sample. For example, fetal cells can be selectively lysed releasing their nuclei when a blood sample including fetal cells is combined with deionized water. Such selective lysis allows for the subsequent enrichment of fetal nuclei using, e.g., size or affinity based separation. In another example platelets and/or enucleated red blood cells are selectively lysed to generate a sample enriched in nucleated cells, such as fetal nucleated red blood cells (fnRBC) and maternal nucleated blood cells (mnBC). The fnRBC's can subsequently be separated from the mnBC's using, e.g., affinity to antigen-i or magnetism differences in fetal and adult hemoglobin. When obtaining a sample from an animal (e.g., blood sample), the amount can vary depending upon animal size, its gestation period, and the condition being screened. In some embodiments, up to 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 mL of a sample is obtained. In some embodiments, 1-50, 2-40, 3-30, or 4-20 mL of sample is obtained. In some embodiments, more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 mL of a sample is obtained. Nucleic acids from samples that can be analyzed by the methods herein include: double-stranded DNA, single-stranded DNA, single-stranded DNA hairpins, DNA/RNA hybrids, RNA (e.g. mRNA or miRNA) and RNA hairpins. Examples of genetic analyses that can be performed on nucleic acids include e-g., SNP detection, STR detection, RNA expression analysis, promoter methylation, gene expression, virus detection, viral subtyping and drug resistance. In some embodiments, less than 1 pg, 5 pg, 10 pg, 20 pg, 30 pg, 40 pg, 50 pg, 100 pg, 200 pg, 500 pg, 1 ng, 5 ng, 10 ng, 20 ng, 30 ng, 40 ng, 50 ng, 100 ng, 200 ng, 500 ng, 1 ug, 5 ug, 10 ug, 20 ug, 30 ug, 40 ug, 50 ug, 100 ug, 200 ug, 500 ug or 1 mg of nucleic acids are obtained from the sample for further genetic analysis. In some cases, about 1-5 pg, 5-10 pg, 10-100 pg, 100 pg-1 ng, 1-5 ng, 5-10 ng, 10-100 ng, 100 ng-1 ug of nucleic acids are obtained from the sample for further genetic analysis. In some embodiments, the methods described herein are used to detect and/or quantified a target nucleic acid molecule. In some embodiments, the methods described herein are used to detect and/or quantified multiple target nucleic acid molecules. The methods described herein can analyzed at least 1, 2, 3, 4, 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, different target nucleic acids. In some embodiments, the methods described herein are used to detect and/or quantify target nucleic acids to profile a specific tissue or a specific condition. In some embodiments, the methods described herein are used to detect and/or quantify target nucleic acids to detect biomarkers for specific tissue or condition. In some embodiments, the methods described herein are used to regulate gene expression. In some embodiments, the methods described herein are use for gene therapy. In some embodiments, the methods described herein are used to detect and/or quantify target nucleic acids to profile a neoplastic and/or cancer cell. In some embodiments, the methods described herein are used to detect and/or quantify target nucleic acids to diagnose cancer and/or a neoplastic condition. In some embodiments, the methods described herein are used to detect and/or quantify target nucleic acids to detect biomarkers in a neoplastic and/or cancer cell. In some embodiments, the methods described herein are used to regulate gene expression in a neoplastic and/or cancer cell. In some embodiments, the methods described herein are used for gene expression. As used herein the term “diagnose” or “diagnosis” of a condition includes predicting or diagnosing the condition, determining predisposition to the condition, monitoring treatment of the condition, diagnosing a therapeutic response of the disease, and prognosis of the condition, condition progression, and response to particular treatment of the condition. In some embodiments, the methods described herein are used to quantify nucleic acid expression in different tissues, developmental lineages and/or different states of a condition. In some embodiments, the methods described herein are used to quantify nucleic acid expression in different states of a neoplastic and/or cancer condition. In some embodiments, the methods described herein are used to detect and/or quantify target nucleic acids without the need of target nucleic acid isolation. In some embodiments, the methods described herein are used to detect and/or quantify a target nucleic acid directly from a nucleic acid sample comprising DNA and RNA molecules. In some embodiments, the methods described herein are used to quantify nucleic acid expression in different tissues, developmental lineages and/or different states of a condition. In some embodiments, the methods described herein are used to quantify nucleic acid expression in different states of a neoplastic and/or cancer condition. In some embodiments, the methods described herein are used to distinguish between target nucleic acids that differ from another nucleic acid by 1 nt. In some embodiments, the methods described herein are used to distinguish between target nucleic acids that differ from another nucleic acid by 1 nt or more than 1, 2, 3, 5, 10, 15, 20, 21, 22, 24, 25, 30 nt. In some embodiments, the methods described herein are used to detect and/or quantified multiple target nucleic acid molecules. The methods described herein can analyzed at least 1, 2, 3, 4, 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, different target nucleic acids. In some embodiments, the methods described herein are used to detect and/or quantify target nucleic acids without the need of target nucleic acid isolation. In some embodiments, the methods described herein are used to detect and/or quantify a target nucleic acid directly from a nucleic acid sample comprising DNA and RNA molecules. In some embodiments, less than 1 pg, 5 pg, 10 pg, 20 pg, 30 pg, 40 pg, 50 pg, 100 pg, 200 pg, 500 pg, 1 ng, 5 ng, 10 ng, 20 ng, 30 ng, 40 ng, 50 ng, 100 ng, 200 ng, 500 ng, 1 ug, 5 ug, 10 ug, 20 ug, 30 ug, 40 ug, 50 ug, 100 ug, 200 ug, 500 ug or 1 mg of nucleic acids are obtained from the sample for further genetic analysis. In some cases, about 1-5 pg, 5-10 pg, 10-100 pg, 100 pg-1 ng, 1-5 ng, 5-10 ng, 10-100 ng, 100 ng-1 ug of nucleic acids are obtained from the sample for further genetic analysis. miRNA In some embodiments, the methods described herein are used to detect and/or quantify microRNAs (miRNAs). New discovered miRNAs are thought to be important in the regulation of gene expression. MiRNA are usually single-stranded RNAs approximately 22 nt long. Without being limited to any theory, these small molecules inhibit protein production through selective binding to the complementary messenger RNA sequences. Although the inhibition-mediated biological function of these miRNA molecules are not yet fully understood, miRNAs seems to be crucial in diverse regulations, including development, cell differentiation, proliferation, apoptosis, and maintenance of stemness and imprinting. Through selective binding to complementary messenger RNA sequences, they can mediate translation repression or RNA degradation. Up to 20%-25% of mammalian genes might be regulated by miRNAs. So far, more than 400 miRNAs have been identified in human genome. Many of them are only different in one or few nucleotides (http://microrna.sanger.ac.uk/sequences/ftp.shtml). In some embodiments, the methods described herein are used to detect and/or quantified a miRNA molecule. In some embodiments, the methods described herein are used to detect and/or quantified multiple miRNA molecules. The methods described herein can analyzed at least 1, 2, 3, 4, 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, different miRNAs. Recent studies have shown that expression of mature miRNAs is tissue-specific and the abundance of miRNAs varies several orders of magnitude. In some cases, expression of miRNAs is tissue-specific, such as the expression of miRNAs miR-1 and miR-133 to be specific to heart and skeletal muscle and miR-122a specific to liver tissue. Moreover, miss-regulation of miRNA expression might contribute to human cancers and miRNAs are considered to be a new class of cellular molecules involved in human oncogenesis. miRNA has been demonstrated to be a new class of cellular molecules involved in human oncogenesis. The first report was made in chronic lymphatic leukemia (CLL) where a number of patients show down-regulation of miRNA-15 and miRNA-16. These studies were followed by studies demonstrating altered expression of miRNA in a number of cancers including colon cancers, Burkitt lymphoma, lung cancer, breast cancer, large cell lymphoma, glioblastoma, B cell lymphoma, hepatocellular carcinoma, and papillary thyroid carcinoma. Expression of mature miRNA is also found to be specific to normal but not cancer cells and tissues. For instance, the expression of mature miR-122a is very low in four liver cancer cell lines and hepatocellular carcinomas, but very high in normal liver tissue. Systemically profiling of miRNA expression displays unique signatures in a number of cancers, such as the difference that can differentiate malignant and non-malignant prostate samples, and discriminate clinically relevant breast cancer phenotypes. In some embodiments, the methods described herein are used to detect and/or quantify miRNAs to profile a specific tissue or a specific condition. In some embodiments, the methods described herein are used to detect and/or quantify miRNAs to detect biomarkers for specific tissue or condition. In some embodiments, the methods described herein are used to regulate gene expression. In some embodiments, the methods described herein are use for gene therapy. In some embodiments, the methods described herein are used to detect and/or quantify miRNAs to profile a neoplastic and/or cancer cell. In some embodiments, the methods described herein are used to detect and/or quantify miRNAs to diagnose cancer and/or a neoplastic condition. In some embodiments, the methods described herein are used to detect and/or quantify miRNAs to detect biomarkers in a neoplastic and/or cancer cell. In some embodiments, the methods described herein are used to regulate gene expression in a neoplastic and/or cancer cell. In some embodiments, the methods described herein are used for gene expression. miRNAs are found in the genomes of humans, animals, plants and viruses. miRNAs are generated from endogenous hairpin-shaped transcripts. In animals, miRNAs are transcribed as long primary transcripts (pri-microRNAs) by RNA polymerase II enzyme. They are cleaved in the nucleus by RNAse III endonuclease Drosha, releasing a ˜60-70 nt stem loop pre-miRNAs. The pre-miRNA is actively transported to the cytoplasm by export receptor exportin-5 where it is processed by the enzyme Dicer yielding a 22 nt microRNA duplexes. Following denaturation by the action of helicases, one strand of the duplex (the mature miRNA) is incorporated into a ribonucleoprotein complex known as RISC(RNA-induced silencing complex), which will guide the particular miRNA to its messenger RNA target to lead to regulation of the corresponding protein. In some embodiments, the methods described herein are used to distinguish precursors miRNA from mature miRNA. The methods described herein can distinguish at least 1, 2, 3, 4, 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, different miRNAs from their precursor. Many miRNA have been identified through both biological approach and informatics analysis. There are total 475 human miRNA genes listed in the miRNA database (http://microrna.sanger.ac.uk/sequences/ftp.shtml) and it is expected to be approximately 1000, which would be equivalent to almost 3% of the protein-coding genes. Many of mature human miRNAs are closely related in sequences and more than 20% are grouped into isoforms with nearly identical sequences, usually differing by 1-3 nt. The largest human isoform families include let-7, including 9 mature molecules with different sequences. These families are designated with a letter (e.g. let-7b and let-7c). Because of the minor difference of isoforms in addition to the small size of the molecules and coexistence with precursors, it is quite challenge to analyze or profile miRNAs. In some embodiments, the methods described herein are used to distinguish between miRNA isoforms. In some embodiments, the methods described herein are used to distinguish between miRNA isoforms that differ by 1 nt. In some embodiments, the methods described herein are used to distinguish between miRNA isoforms that differ by more than 1, 2, 3, 5 nt. The methods described herein can distinguish between at least 1, 2, 3, 4, 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, different miRNAs isoforms. Distinguished miRNA expression has found in the different tissues, developmental lineages and differentiation states of various human malignancies. In some embodiments, the methods described herein are used to quantify miRNA expression in different tissues, developmental lineages and/or different states of a condition. In some embodiments, the methods described herein are used to quantify miRNA expression in different states of a neoplastic and/or cancer condition. In some embodiments, the method described herein are used to detect and/or quantify miRNA when less than 1 pg, 5 pg, 10 pg, 20 pg, 30 pg, 40 pg, 50 pg, 100 pg, 200 pg, 500 pg, 1 ng, 5 ng, 10 ng, 20 ng, 30 ng, 40 ng, 50 ng, 100 ng, 200 ng, 500 ng, 1 ug, 5 ug, 10 ug, 20 ug, 30 ug, 40 ug, 50 ug, 100 ug, 200 ug, 500 ug or 1 mg of nucleic acids are obtained from the sample for further genetic analysis. In some cases, about 1-5 pg, 5-10 pg, 10-100 pg, 100 pg-1 ng, 1-5 ng, 5-10 ng, 10-100 ng, 100 ng-1 ug of nucleic acids are obtained from the sample. In some cases, about 1-5 pg, 5-1 0 pg, or 10-100 pg of nucleic acids are obtained from the sample for further analysis according to methods described herein. In some embodiments, the methods described herein are used to detect and/or quantify miRNA without the need of miRNA isolation. In some embodiments, the methods described herein are used to detect and/or quantify miRNA without the need of RNA isolation. In some embodiments, the methods described herein are used to detect and/or quantify miRNA directly from a nucleic acid sample comprising DNA and RNA molecules. Oligonucleotide Ligation Assay In one aspect of the invention a set of oligonucleotides is designed to detect a target nucleic acid. FIG. 1 shows an embodiment of the invention in which a pair of oligonucleotides (depicted as oligo 1 and oligo 2 in FIG. 1) binds to a target miRNA. Even though FIG. 1 depicts a process for miRNA detection, the methods described herein can also be used in other analysis, including STR and SNP detection, RNA expression analysis, promoter methylation, gene expression, virus detection, viral subtyping and drug resistance. In some embodiments the set of oligonucleotide probes comprises a first oligonucleotide probe having a 5′ target specific region and a 3′ universal sequence region (depicted as oligo 1 in FIG. 1), and a second probe having a 3′ target specific region and a 5′ universal promoter region (depicted as oligo 2 in FIG. 1). In some embodiments, the first and the second oligonucleotide probes are suitable for ligation together when hybridized adjacent to one another to said target nucleic acid as shown in FIG. 1. In some embodiments the set of oligonucleotide probes comprises a first oligonucleotide probe having a 5′ target specific region and a 3′ universal sequence region (depicted as oligo 1 in FIG. 2), a second probe having a 3′ target specific region and a 5′ universal sequence region (depicted as oligo 2 in FIG. 2), a third oligonucleotide probe having a 5′ region specific to the first 3′ universal sequence region in the first probe (depicted as oligo 4 in FIG. 2), and a fourth probe having a 3′ region specific to the 5′ universal sequence region of said second oligonucleotide probe (depicted as oligo 3 in FIG. 2). In some embodiments, the first and said second oligonucleotides probes are suitable for ligation together when hybridized adjacent to one another to said target nucleic acid, and the third and the fourth oligonucleotides probes are suitable for ligation to the target nucleic acid when hybridized adjacent to said nucleic acid target. Specifically, the 5′ region of the first oligonucleotide probe anneals to the 5′ region of said target nucleic acid such that the target specific region of said first oligonucleotide probe is aligned with the 5′ region of said target nucleic acid and the 3′ region of the second oligonucleotide probe anneals to the 3′ region of said target nucleic acid such that the target specific region of said second oligonucleotide probe is aligned with the 3′ region of said target nucleic acid. Furthermore, the 3′ end of the third oligonucleotide probe and the 5′ end of the fourth oligonucleotides probe are suitable for ligation to target nucleic acid when the 3′ end of the third oligonucleotide is hybridized adjacent to the 5′ end of the target nucleic acid and the 5′ end of the fourth oligonucleotides probe is hybridized adjacent to the 3′ downstream end of the target nucleic acid. In some embodiments, the set of oligonucleotide probes comprises a first oligonucleotide probe having a 5′ target specific region and a 3′ universal sequence region (depicted as oligo 1 in FIG. 1 and FIG. 2). The universal region in oligo 1 can be the sequence of a promoter. In some embodiment, the promoter sequence in oligo 1 is a promoter for a DNA polymerase. Examples of DNA polymerase include, but are not limited to, Thermoanaerobacter thermohydrosulfuricus DNA polymerase, Thermococcus litoralis DNA polymerase I, E. coli DNA polymerase I, Taq DNA polymerase I, Tth DNA polymerase I, Bacillus stearothermophilus (Bst) DNA polymerase, E. coli DNA polymerase III, bacteriophage T5 DNA polymerase, bacteriophage M2 DNA polymerase, bacteriophage T4 DNA polymerase, bacteriophage T7 DNA polymerase, bacteriophage phi29 DNA polymerase, bacteriophage PRD1 DNA polymerase, bacteriophage phi15 DNA polymerase, bacteriophage phi21DNA polymerase, bacteriophage PZE DNA polymerase, bacteriophage PZA DNA polymerase, bacteriophage Nf DNA polymerase, bacteriophage M2Y DNA polymerase, bacteriophage B103 DNA polymerase, bacteriophage SF5 DNA polymerase, bacteriophage GA-1 DNA polymerase, bacteriophage Cp-5 DNA polymerase, bacteriophage Cp-7 DNA polymerase, bacteriophage PR4DNA polymerase, bacteriophage PR5DNA polymerase, bacteriophage PR722DNA polymerase and bacteriophage L17 DNA polymerase. In some embodiments, the promoter sequence in oligo 1 is a promoter for a phage polymerase. Examples of phage polymerase include, but are not limited to, T7 RNA polymerase, T3 RNA polymerase or SP6 RNA polymerase. In some embodiments, the universal sequence can be used to capture or detect the oligonucleotide set as described herein. In some embodiments, the set of oligonucleotide probes comprises a second oligonucleotide probe having a 3′ target specific region and a 5′ universal region (depicted as oligo 2 in FIG. 1 and FIG. 2). The universal region in oligo 1 can be the sequence of a promoter as described above. In some embodiments, the universal sequence can be used to capture or detect the oligonucleotide set as described herein. In some embodiments, the set of oligonucleotide probes comprises a first oligonucleotide probe having in a 3′ to 5′ order a universal sequence region, a tag region and a target specific region (depicted as oligo 1 in FIGS. 1 and 2), where the universal region can be a promoter as described above. In some embodiments, the universal sequence can be used to capture or detect the oligonucleotide set as described herein. In some embodiments, the tag region of oligo 1 can be a unique sequence assigned to a specific target nucleic acid. The tag sequence can be used to capture or detect the oligonucleotide set as described herein. In some embodiments where the first oligonucleotide has a tag region, the third oligonucleotide probe has a 3′ region that is specific to the tag region of the first oligonucleotide probe (depicted as oligo 4 in FIG. 3). In some embodiments where the first oligonucleotide has a tag region, the probe set further comprises a fifth oligonucleotide probe that is specific to the tag region of said first oligonucleotide probe (depicted as oligo 5 in FIG. 7). In some embodiments, the set of oligonucleotide probes comprises a second oligonucleotide probe having in a 5′ to 3′ order a universal sequence region, a tag region and a target specific region (depicted as oligo 2 in FIGS. 1 and 2), wherein the universal sequence region can be a promoter region as described above. In some embodiments, the tag region of oligo 2 can be a unique sequence assigned to a specific target nucleic acid. The tag sequence can be used to capture or detect the oligonucleotide set as described herein. In some embodiments where the second oligonucleotide has a tag region, the fourth oligonucleotide probe has a 5′ region that is specific to the tag region of the second oligonucleotide probe (depicted as oligo 3 in FIG. 3). In some embodiments where the second oligonucleotide has a tag region, the probe set further comprises a sixth oligonucleotide probe that is specific to the tag region of said second oligonucleotide probe (depicted as oligo 6 in FIG. 7). For simplicity, most of the examples and embodiments of the invention will be illustrated using a set of oligonucleotide probes containing a first, a second, a third and a fourth probe named oligo 1, oligo 2, oligo 4 and oligo 3 throughout the examples and embodiments described herein. However, as described above a probe set containing less than four probes or more than four probes are encompassed in the methods described herein. In some embodiments, at least three oligonucleotides are designed to detect a target nucleic acid. In some embodiments, two pairs of oligonucleotides are designed to detect a target nucleic acid. In some embodiments, three pairs of oligonucleotides are designed to detect a target nucleic acid. In some embodiments, a set of two oligonucleotide probes binds to a target nucleic acid (as depicted in FIG. 1 as oligo 1 and 2). In some embodiments, a set of four oligonucleotide probes binds to a target nucleic acid (as depicted in FIG. 2 as oligos 1-4). In some embodiments, any of the oligos have a capturing portion to separate the oligos bound to the target nucleic acid. The capturing portion can be a marker or a capturing sequence. In some embodiments, the capturing portion is a capturing sequencing. The capturing sequence can be the universal sequence of oligo 1 or oligo 2 or the tag sequence of either oligo 1 or 2 as described above. The capturing sequence can be a new portion in oligo 1 or oligo 2 distinct from the universal sequence or tag sequences described above. The capturing sequence can be the universal sequence of oligo 3 or oligo 4 or the tag sequence of either oligo 3 or 4 as described above. The capturing sequence can be a new portion in oligo 3 or oligo 4 distinct from the universal sequence or tag sequences described above. In some embodiments, a capturing sequence is introduced at oligo 1, which can be captured by capturing sequence-conjugated to a solid structure such as beads or an oligonucleotide array. In some embodiments, a capturing sequence is introduced at oligo 2, which can be captured by capturing sequence-conjugated to a solid structure such as beads or an oligonucleotide array. In some embodiments, a capturing sequence is introduced at oligo 3, which can be captured by capturing sequence-conjugated to a solid structure such as beads or an oligonucleotide array. In some embodiments, a capturing sequence is introduced at oligo 4, which can be captured by capturing sequence-conjugated to a solid structure such as beads or an oligonucleotide array. In some embodiments, the capturing portion is a marker. Markers that are used to capture oligos are known in the art. The marker then can be captured by in a subsequent isolation step by a marker-binding solid structure. In some embodiments the marker is biotin. In some embodiments, biotin is introduced at oligo 1, which can be captured by streptavidin-conjugated to a solid structure such as beads. In some embodiments, biotin is introduced at oligo 2, which can be captured by streptavidin-conjugated to a solid structure such as beads. In some embodiments, biotin is introduced at oligo 3, which can be captured by streptavidin-conjugated to a solid structure such as beads. In some embodiments, biotin is introduced at oligo 4, which can be captured by streptavidin-conjugated to a solid structure such as beads. Biotin can be introduced at any of the oligos by annealing a primer containing biotin to the universal sequence of the oligos. Alternatively, biotin can be introduced at any of the oligos when the oligos are synthesized by methods known in the art. In some embodiments, oligo 1 will have a phosphate group at its 5′ end. In some embodiments, oligo 1 and oligo 3 will have a phosphate group at its 5′ end. Optionally, oligo 2 will have a T7 promoter at its 5′ end. In some embodiments, when oligo 1 and oligo 2 simultaneously bind to one target nucleic acid molecule, e.g., miRNA, they are ligated according to techniques to known in the art. In some embodiments, when oligo 1 and oligo 2 simultaneously bind to one target nucleic acid molecule, and oligo 4 and oligo 3 bind to oligo 1 and 2, respectively, they are ligated according to techniques to known in the art. For example, the oligos can be ligated by T4 DNA ligase. When oligos are stacking together to bind to a molecule with a perfect match at the junction at their ends, it results in a specific binding to the targeted nucleic acid, e.g., mRNA. The stacking oligos can be ligated to form a ligated product, which can be used for detection. Without being limited to any theory, any sequence-closely related to the target nucleic acid molecules will either block the ligation or prevent the hybrid formation. Therefore, isoforms can be distinguished in the assay. If the difference is in the middle of the target nucleic acid, it will block the ligation and detection, although the hybrids are able to form. In some embodiments multiple nucleic acids are analyzed by mixing multiple oligo sets together, each of which is specific to one nucleic acid target. In some embodiments, either one of oligo 1, oligo 2, oligo 3 or oligo 4 have a capturing portion to separate the oligos as described above. In some embodiments, after oligo 1 and 2, or oligo 1, oligo 2, oligo 3 and oligo 4 have been ligated the ligated product will be separated using the capturing portion in any of the oligos. After separation, the ligated products can then detached from the duplexes and analyzed according to the methods described herein In some embodiments, the use of the set of oligonucleotides probes described herein allow for the detection of mature nucleic acids. For instance, miRNA precursors contain the identical sequence of a mature miRNA, hence, they can be targeted by the pair oligos represented as oligo 1 and 2 in FIG. 1, leading to ligation and detection. Either oligo 1 or 2 can be extended with a universal sequence and/or a unique tag sequence, corresponding to the sequence of oligo 3 or oligo 4. The oligo with the extended universal sequence and/or unique tag sequence will form a partial duplex with a protruding sequence, which is able to hybrid a part of a target nucleic acid molecule. If the target is a mature nucleic acid, e.g., miRNA molecule, the hybridization forms a perfect match with the oligo 3 or oligo 4 at the end of the miRNA, leading to a ligation. If the target is a precursor miRNA, no perfect match end is formed at the junction between the precursor and oligo 3 or oligo 4, and therefore no ligation can occur and no detection can be made. Furthermore, any nucleotide difference that exists at the ends among miRNA isoforms will result in imperfect match, which blocks either the formation of a hybrid or the ligation. In some embodiments, either oligo 1 and 2 can be extended with a unique tag sequence, corresponding to a region of oligo 4 and oligo 3, respectively (see FIG. 3). In some embodiments, either oligo 1 and 2 can be extended with a unique tag sequence, corresponding to the sequences of oligo 5 and oligo 6, respectively (see FIG. 7) In some embodiments, at least two pairs of oligonucleotides allow for the detection of mature nucleic acids. For instance, miRNA precursors can be targeted by the pair oligos represented as oligo 1 and 2 in FIGS. 1 and 2, leading to ligation and detection. Oligo 1 and 2 are extended with universal sequences and/or two unique tag sequences, corresponding to the sequence of oligo 3 and 4 (FIG. 2). These oligos form two partial duplexes with a protruding sequence, each of which is able to hybrid a part of a target nucleic acid molecule. If the target is a mature nucleic acid, e.g, miRNA molecule, the hybridization forms two perfect matches with oligo 3 and oligo 4 at the ends of the miRNA (FIG. 2), leading to a ligation. If the target is a precursor miRNA, no perfect match ends are forming at the junctions between the precursor and oligo 3 and/or between the precursor and oligo 4, and therefore no ligation can occur and no detection can be made. Furthermore, any nucleotide difference that exists at the ends among miRNA isoforms will result in imperfect match, which blocks either the formation of a hybrid or the ligation. In some embodiments, at least three pairs of oligonucleotides allow for the detection of mature nucleic acids. For instance, miRNA precursors can be targeted by the pair oligos represented as oligo 1 and 2 in FIGS. 1 and 2, leading to ligation and detection. Oligo 1 and 2 are extended with universal sequences and two unique tag sequences, corresponding to the sequence of oligo 3, 4, 5 and 6 (FIG. 7). These oligos form two partial duplexes with a protruding sequence, each of which is able to hybrid a part of a target nucleic acid molecule. If the target is a mature nucleic acid, e.g, miRNA molecule, the hybridization forms two perfect matches with oligo 5 and oligo 6 at the ends of the miRNA (FIG. 7), leading to a ligation. If the target is a precursor miRNA, no perfect match ends are forming at the junctions between the precursor and oligo 5 and/or between the precursor and oligo 6, and therefore no ligation can occur and no detection can be made. Furthermore, any nucleotide difference that exists at the ends among miRNA isoforms will result in imperfect match, which blocks either the formation of a hybrid or the ligation. In some embodiments multiple nucleic acids are analyzed by mixing multiple oligo sets together, each of which is specific to one nucleic acid target. Each nucleic acid molecule will initiate the formation of a duplex and multiple nucleic acid lead to the assembly of multiple duplexes. For simplicity, some of the embodiments described herein used two pairs of oligonucleotides to detect the target nucleic acids. However, the invention encompasses the use of at least 3, 4, 5, 6, 7, 8 9,
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