Binding and expression target analysis (BETA) is a software package that integrates ChIP-seq of TFs or chromatin regulators with differential gene expression data to infer direct target genes. The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive
[user@cn3111 ~]$ module load BETA
[user@cn3111 ~]$ BETA -h
usage: BETA [-h] [--version] {basic,plus,minus} ...
BETA --- Binding Expression Target Analysis
positional arguments:
{basic,plus,minus} sub-command help
basic Main BETA Function: Transcription factors direct targets
prediction.
plus The super beta beta can not only do TF's direct targets
and active or repressive prediction, but also do the
motif analysis with the target regions
minus Find Target Genes with only binding data: regulatiry
potential score
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
For command line options of each command, type: BETA COMMAND -h
Download sample data:
[user@cn3111 ~]$ cp $BETA_DATA/* .Link a human genome sequence in FASTA format to the current folder:
[user@cn3111 ~]$ ln -s /fdb/igenomes/Homo_sapiens/UCSC/hg19/hg19.faBETA Basic will do the factor function prediction and direct target detecting:
[user@cn3111 ~]$ BETA basic -p 3656_peaks.bed -e AR_diff_expr.xls -k LIM -g hg19 --da 500 -n basic --info 1,2,6 [09:09:02] Argument List: [09:09:02] Name = basic [09:09:02] Peak File = 3656_peaks.bed [09:09:02] Top Peaks Number = 10000 [09:09:02] Distance = 100000 bp [09:09:02] Genome = hg19 [09:09:02] Expression File = AR_diff_expr.xls [09:09:02] Expression Type = MicroArray, LIMMA result [09:09:02] Number of differential expressed genes = 500.0 [09:09:02] Differential expressed gene FDR Threshold = 1 [09:09:02] Up/Down Prediction Cutoff = 0.001000 [09:09:02] Function prediction based on regulatory potential [09:09:02] Check 3656_peaks.bed successfully! [09:09:02] #ID logFC AveExpr t P.Value adj.P.Val B is the header of the expression file [09:09:02] Checking the differential expression infomation... [09:09:02] Take the first line with Differential Information as an example: NR_045762_at3.16711734 9.140369116 35.91057535 6.99E-11 4.18E-07 14.13456018 [09:09:02] Differential Expression file format successful passed [09:09:02] You do not like filter peak by CFCT boundary, it will be filtered only by the distance [09:09:02] Read file <3656_peaks.bed> OK! All <7059> peaks. [09:09:09] Process <50801> genes [09:09:16] Finished! Preliminary results saved into temporary file:BETA Plus will do TF active and repressive function prediction, direct targets detecting and motif analysis in target regions:[15841, 18956] [09:09:16] Genes were seprated to two parts: up regulated and down regulated. cut: write error: Broken pipe cut: write error: Broken pipe [09:09:17] Prepare file for the Up/Down Test null device 1 [09:09:20] Finished, Find the result in basic_function_prediction.pdf [09:09:20] Get the Rank Product of the "upregulate" genes ['"upregulate"'] [09:10:00] pick out the peaks 100000bp around the selected genes ... total time: 0:0:58
[user@cn3111 ~]$ BETA plus -p 3656_peaks.bed -e AR_diff_expr.xls -k LIM -g hg19 --gs hg19.fa [08:38:05] Argument List: [08:38:05] Name = NA [08:38:05] Peak File = 3656_peaks.bed [08:38:05] Top Peaks Number = 10000 [08:38:05] Distance = 100000 bp [08:38:05] Genome = hg19 [08:38:05] Expression File = AR_diff_expr.xls [08:38:05] Genome Sequence fasta formated data = hg19.fa [08:38:05] Expression Type = MicroArray, LIMMA result [08:38:05] Number of differential expressed genes = 0.5 [08:38:05] Differential expressed gene FDR Threshold = 1 [08:38:05] Up/Down Prediction Cutoff = 0.001000 [08:38:05] Function prediction based on regulatory potential [08:38:05] Check 3656_peaks.bed successfully! [08:38:05] #ID logFC AveExpr t P.Value adj.P.Val B is the header of the expression file [08:38:05] Checking the differential expression infomation... [08:38:05] Take the first line with Differential Information as an example: NR_045762_at3.16711734 9.140369116 35.91057535 6.99E-11 4.18E-07 14.13456018 [08:38:05] Differential Expression file format successful passed [08:38:05] You do not like filter peak by CFCT boundary, it will be filtered only by the distance [08:38:06] Read file <3656_peaks.bed> OK! All <7059> peaks. [08:38:13] Process <50801> genes [08:38:20] Finished! Preliminary results saved into temporary file:End the interactive session:[15841, 18956] [08:38:20] Genes were seprated to two parts: up regulated and down regulated. cut: write error: Broken pipe cut: write error: Broken pipe [08:38:20] Prepare file for the Up/Down Test null device 1 [08:39:05] Finished, Find the result in NA_function_prediction.pdf [08:39:05] Get the Rank Product of the "upregulate" genes ['"upregulate"'] [08:39:35] pick out the peaks 100000bp around the selected genes ... [08:39:36] get three regions of every peak around the up genes ['up_middle.bed', 'up_left.bed', 'up_right.bed'] [08:40:42] get the fasta format sequence data of the three regions of up [08:40:42] get three regions of every peak around the non genes ['non_middle.bed', 'non_left.bed', 'non_right.bed'] [08:41:46] get the fasta format sequence data of the three regions of non [08:41:46] run mis to do the known motif scan with cistrome motif database Calculating Background.. A or T: 161685 C or G: 131715 Others: 0 Calculating Background.. A or T: 161503 C or G: 130430 Others: 0 Calculating Background.. A or T: 159938 C or G: 131995 Others: 0 Calculating Background.. A or T: 236519 C or G: 149281 Others: 0 Calculating Background.. A or T: 236826 C or G: 147045 Others: 0 Calculating Background.. A or T: 235215 C or G: 148656 Others: 0 [08:43:51] T statistic test performed here to do the significance testing of every motif [09:05:12] motif result will be in html format ... Success parser from table. [09:05:20] Done: find motif result in beatmotif.html file ... total time: 0:27:14
[user@cn3111 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$