1. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

2. Searching for transcription factor binding sites with TRANSFAC George Bell, Ph.D. Bioinformatics and Research Computing Hot Topics – October 2009

3. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Outline What is known about your favorite TFs? In what regulatory DNA should we search? How can we search for an inexact sequence motif like a TFBS? What related resources are available?

4. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Transcription control is complex Lodish et al. Molecular Cell Biology. Model for cooperative assembly of an activated transcription-initiation complex at the TTR promoter in hepatocytes Kettenberger et al., 2004. (1y1w) Complete RNA Polymerase II elongation complex (12 subunits)

5. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics TRANSFAC at Biobase Connect from Whitehead network

6. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics TRANSFAC introduction created in 1988 contains information about transcription factors that have been experimentally determined to bind DNA includes eukaryotic cis-acting regulatory DNA elements and trans-acting factors, in organisms ranging from yeast to humans. The majority of information has been manually curated from the primary literature.

7. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Browsing transcription factors Select species Detailed info

8. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Types of TRANSFAC data Gene – curated info Promoter – TSS coordinates from Ensembl, FANTOM, etc. Functional Region – describes publushed regulatory regions Composite Element (with two or more nearby binding sites) Site – describes published TFBSs ChIP-chip – shows data by target Matrix – contains published aligned binding sites and positional probabilities

9. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Transcription factor matrix ACGTConsensus 1220S 2120R 3011A 0500C 5000A 0041G 0140G 0005T 0050G 0122K 0203Y 1031G Example: V$MYOD_01vertebrate MyoD matrix 1

10. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Matrix identifiers Examples: V$MYOD_01, V$AP1_Q4_01 V$ = vertebrate I$ = insects; P$ = plants; F$ = fungi; N$ = nematodes; B$ = bacteria MYOD = factor or family name 01 = matrix number 1 for MYOD Q* = matrix reliability/quality (1 – 6) 1Functionally confirmed transcription factor binding site 2Binding of pure protein (purified or recombinant) 3Immunologically characterized binding activity of a cellular extract 4Binding activity characterized via a known binding sequence 5Binding of uncharacterized extract protein to a bona fide element 6No quality assigned

11. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Matrices are redundant V$MYOD_01 V$MYOD_Q6 V$MYOD_Q6_01

12. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Extracting regulatory regions One, many or all genes? Promoters or all potential regions (introns, intergenic)? Sources of genomic sequence: –UCSC genome browser (click on “DNA”) –Ensembl BioMart (“Sequences” for output) –Published datasets

13. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Starting MATCH

14. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics MATCH profiles (sets of matrices) Taxon: all bacteria fungi insects invertebrates nematodes plants vertebrate_non_redundant vertebrate_non_redundant_minFN vertebrate_non_redundant_minFP vertebrate_non_redundant_minSUM vertebrates Tissue: adipocyte_specific immune_cell_specific liver_specific lung_specific muscle_specific nerve_system_specific pancreatic_beta_cell_specific pituitary_specific redox_specific Biological process: cell_cycle_specific User defined: Muscle_george

15. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics MATCH output Core == first 5 most conserved positions

16. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Creating a custom matrix: input

17. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Creating a custom matrix: output

18. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics MATCH Profiler - input

19. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics MATCH Profiler - output

20. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics MATCH with our custom profile

21. Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics Related resources UCSC Genome Browser (hg18): –“TFBS Conserved” track (human/mouse/rat) JASPAR (public database of transcription factor binding profiles): –http://jaspar.genereg.net/ Create a sequence logo: http://weblogo.berkeley.edu Command-line tools: –TRANSFAC; tffind; HMMER1; MAST (MEME Suite) Search for “patterns” ( ex: CAxxTGx[TC] ) –EMBOSS: fuzznuc; dreg