人类转录因子靶基因的数据整合研究.docx

Abstract The regulation of gene expression contains a series of basic and complex biological processes. It can be divided into five levels of complex controls, which are transcriptional level, transcriptional level, post-transcriptional level, translational level and post-translational level One of the most important and complex regulations happens at the transcriptional level? Both DNA elements and transcription factors (TFs) could regulate the initiation of transcription. With the development and application of ChlP-chip and ChlP-seq techniques, there are huge high-throughput data of genome-wide cis? regulatory elements and binding TFs available? A large amount of raw data or well- annotated data were accumulated in the database of NCBI GEO and ENCODE. In order to obtain the information of TFs and their TF targets, we collected and integrated these data sets. We perfomied keywords searches over the GEO and ENCODE databases to find the TF binding DNA datasets, which excluded data of histone modification and general transcription factors, e.g. H3K4me3 and POLR2A? Based on the text mining from the web files, we obtained 958 datasets from GEO and 614 datasets from ENCODE. We downloaded all the raw or well-annotated data from the 1567 datasets totally. We have constnicted a pipeline for processing the collected ChlP-seq data. We performed sequence alignments to the reference genome with the Bowtie software and integrated these data sets with the SAMtools software. Then we used the MACS software to call peaks for each transcription factor. As a result, we collected 1,567 large scale datasets for 234 humanTFs. After analysis, we obtained a large amount of TF binding site peaks for the 234 TFs from these datasets. Through data integration and analysis, we provided an important resource for futher study of TF targets and TF regulation. Key words: TFs TF targets ChlP-seq ChlP-chip 摘要 Abstract II Abstract II 2.2ChIP数据的收集与整合 (17) 2.2 ChIP数据的收集与整合 (17) 2.3 ChIP数据的分析与处理 (20