ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
| العنوان: | ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor |
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| المؤلفون: | Junwen Wang, Michael Q. Zhang, Panwen Wang, Mulin Jun Li, Jing Qin |
| المصدر: | Nucleic Acids Research |
| سنة النشر: | 2011 |
| مصطلحات موضوعية: | Chromatin Immunoprecipitation, Microarray, Transcription Factors - metabolism, Computational biology, Biology, DNA sequencing, Mice, Gene expression, Genetics, Animals, Humans, Regulatory Elements, Transcriptional, Transcription factor, Oligonucleotide Array Sequence Analysis, Binding Sites, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Articles, Gene expression profiling, DNA binding site, ComputingMethodologies_PATTERNRECOGNITION, Gene chip analysis, Chromatin immunoprecipitation, Software, Transcription Factors |
| الوصف: | Chromatin immunoprecipitation (ChIP) coupled with high-throughput techniques (ChIP-X), such as next generation sequencing (ChIP-Seq) and microarray (ChIP-chip), has been successfully used to map active transcription factor binding sites (TFBS) of a transcription factor (TF). The targeted genes can be activated or suppressed by the TF, or are unresponsive to the TF. Microarray technology has been used to measure the actual expression changes of thousands of genes under the perturbation of a TF, but is unable to determine if the affected genes are direct or indirect targets of the TF. Furthermore, both ChIP-X and microarray methods produce a large number of false positives. Combining microarray expression profiling and ChIP-X data allows more effective TFBS analysis for studying the function of a TF. However, current web servers only provide tools to analyze either ChIP-X or expression data, but not both. Here, we present ChIP-Array, a web server that integrates ChIP-X and expression data from human, mouse, yeast, fruit fly and Arabidopsis. This server will assist biologists to detect direct and indirect target genes regulated by a TF of interest and to aid in the functional characterization of the TF. ChIP-Array is available at http://jjwanglab.hku.hk/ChIP-ArrayTest, with free access to academic users. © 2011 The Author(s). published_or_final_version |
| تدمد: | 1362-4962 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b4ce0699f1999f2ee6d74649168b3b2bTest https://pubmed.ncbi.nlm.nih.gov/21586587Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....b4ce0699f1999f2ee6d74649168b3b2b |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13624962 |
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