FAQ:
1.Why Cistrome CR?
A: Hundreds of chromatin regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications. Yet the rules governing these key biological processes remain missing, hidden, or too scattered to find among huge amounts of ChIP-seq data. As an initiative toward a comprehensive understanding for the biological function of chromatin regulator and related histone modifications, Cistrome CR was developed to fill this gap.
2.What’s in Cistrome CR?
A: It is a knowledge-base which covers different kinds of chromatin regulators and related histone modifications based on analyzing a vast amount of ChIP-seq experiments for human and mouse (see Data sources and processing methods Section). Not only basic information such as alias, introduction, biological function, disease association from literature for a single CR, but also the ChIP-seq data information and the analysis result, including motif enrichment, sequence conservation, genomic distribution and relationship between the CRs (reader,writer and eraser) and their related histone modifications were provided.
3.What categories can CRs be divided into?
A: According to their biological function and mechanism of action, CRs are mainly classified into four types: reader, writer, eraser and remodeler. The first three are respectively responsible for recognizing, adding and removing histone modifications, thus affecting the transcriptional activity and gene expression; the last one is ATP-dependent and responsible for reorganizing the structure of chromatin.
4.How to use?
A: Detailed instruction was provided in Quick Start.
5.How about the data visualization and accession?
A: Not only the result figures for every single CR, but also the peak file(.bed) and reads density file(.bw) are free to download, which could be visualized through some other software, such as UCSC Genome Browser.
6.What are data sources?
A: Writers and erasers were collected from Histone database. Readers were derived from Yun M et al ’s work [PMID: 3131977]. Remodelers were retrieved from the research of Y Bao et al [PMID: 17482554].
7.Why are some of the CRs' comparison buttons unclickable?
A: The comparison buttons become unclickable suggests that this dataset of CR has no related histone modifications ChIP-seq data under the same condition.
8.What are the tools and parameters used for analyzing the ChIP-Seq data?
A: Tools and parameters are shown below.
| Tool | Usage | Input | Output | Shell Command |
|---|---|---|---|---|
| Bowtie (0.12.7) | Map reads to genome. | {genome_index}, {treatment_file} | {mapped_sam} | bowtie -m 1 -S {genome_index} {treatment_file} {treatment_name} |
| Samtools | Convert bowtie's output to BAM format. | {mapped_sam},{chrom_len} | {mapped_bam} | samtools view -bt {chrom_len} {mapped_sam} -o {mapped_bam} |
| Merge samples which are replicates. | {mapped_bam1}, {mapped_bam2}, [...] | {combined_bam} | samtools merge {combined_bam} {mapped_bam1} {mapped_bam2} [...] | |
| BEDTools | Find the overlap regions of bdg files generated by MACS and the chromosome length bed file. | {bdg},{chrom_len} | {overlapped_bdg} | intersect -a {bdg} -b {chrom_len} -wa -f 1.00 |
| MACS2 (2.0.10) | Call peaks. | {combined_bam_treatment}, {combined_bam_control} | {bed_peak}, {bed_summit}, {bedgraph} | macs2 callpeak -B -q 0.01 --keep-dup 1 --shiftsize=73 --nomodel -t {combined_bam_treatment} -c {combined_bam_control} -n {description} |
| bedGraphToBigWig | Convert bedgraph into bigwiggle format. | {bedgraph}, {chrom_len} | {bigwig} | bedGraphToBigWig {bedgraph_profile} {chrom_len} {bigwig} |
| MDSeqPos | Discover transcripion factor binding motifs from ChIP-Seq peaks. | {top1000_bed_peak} | {enriched_motif_html} | MDSeqPos -d -w 600 -p 0.001 -m cistrome.xml -s {species} {top1000_bed_peak} {genome_version} |
| CEAS | Perform cis-regulatory element annotation. | {bed_peak}, {wiggle_file}, {gene_table} | {ceas_report} | ceas --name {description} {gene_table} -b {bed_peak} -w {wiggle_file} |
| ConservationPlot | Draw conservation plot on peak summits. | {bed_summit}, {phast_cons} | {conservation_plot} | conservation_plot.py -d {phast_cons} -l Peak_summits {bed_summit} |
