STAT115, 2014 BETA, Galaxy, Cistrome Python regular expression

1. STAT115, 2014 BETA, Galaxy, Cistrome Python regular expression Lin Liu Yang Li

2. Integrative Analysis Differential gene expression Transcription factor binding sites What’s next? One option is “target analysis”: trying to sort out which genes are regulated by a certain protein

3. BETA Three main functions: Predicting TF functions: active or repressive Predicting the target gene of a TF Searching for motif around targeted genes, and predicting potential cooperative factors

4. BETA $ module load centos6/BETA_1.0.5 $ BETA basic –p 3656_peaks.bed –e AR_diff_expr.xls–k LIM –g hg19 --da 500 –n basic

5. Integrative Analysis - Cistrome

6. Galaxy

7. Python: Regular expression import re sequence = ‘AGGCTAGGTCGAT’ re.findall(‘A.G’, sequence) line = "Cats are smarter than dogs" matchObj = re.match( r'(.*) are (.*?) .*', line, re.M|re.I) if matchObj: print "matchObj.group() : ", matchObj.group() print "matchObj.group(1) : ", matchObj.group(1) print "matchObj.group(2) : ", matchObj.group(2) else: print "No match!!"

8. Python: Objects and classes