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Searching for transcription factor binding sites with TRANSFAC. George Bell, Ph.D. Bioinformatics and Research Computing Hot Topics – October 2009. Outline. What is known about your favorite TFs? In what regulatory DNA should we search?

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searching for transcription factor binding sites with transfac

Searching for transcription factor binding sites withTRANSFAC

George Bell, Ph.D.

Bioinformatics and Research Computing

Hot Topics – October 2009

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

outline
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?

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

transcription control is complex
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)

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

transfac at biobase
TRANSFAC at Biobase

Connect from Whitehead network

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

transfac introduction
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.

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

browsing transcription factors
Browsing transcription factors

Select species

Detailed

info

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

types of transfac data
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

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

slide9

Transcription factor matrix

Example: V$MYOD_01 vertebrate MyoD matrix 1

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

matrix identifiers
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)

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

matrices are redundant
Matrices are redundant

V$MYOD_01

V$MYOD_Q6

V$MYOD_Q6_01

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

extracting regulatory regions
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

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

starting match
Starting MATCH

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

match profiles sets of matrices
MATCH profiles (sets of matrices)

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

match output
MATCH output

Core == first 5 most conserved positions

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

creating a custom matrix input
Creating a custom matrix: input

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

creating a custom matrix output
Creating a custom matrix: output

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

match profiler input
MATCH Profiler - input

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

match profiler output
MATCH Profiler - output

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

match with our custom profile
MATCH with our custom profile

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics

related resources
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

Searching for TFBSs with TRANSFAC - Hot topics in Bioinformatics