UCSC Genome Browser - University of Pittsburgh

Report
Regulation of Gene Expression
13 February, 2013
Ansuman Chattopadhyay, PhD
Head, Molecular Biology Information Services
Health Sciences Library System
University of Pittsburgh
[email protected]
Topics

retrieve promoter sequences

determine transcription factor occupancy

browse through the epigenetic biochemical
markers
Histone modifications, DNA methylation etc.,
-predict the location of enhancers, silencers and promoters
Major Topics

identify microRNA that have been
reported or predicted to interact with a
gene
Tools

identify promoter sequence(s) present in your gene of interest

Biobase Transpro

UCSC genome browser

predict transcription factor binding sites

Transfac (Biobase Match)

Browse through the epigenomic markers

ENCODE
Human Epigenome Atlas

identify miRNA that have been reported or predicted to interact with a
gene

Mirtarbase

Mirbase
http://www.hsls.pitt.edu/guides/genetics
An excellent movie on transcription
http://vcell.ndsu.edu/animations/transcription/index.htm
http://www.hsls.pitt.edu/guides/genetics
Promoter, Enhancer and Silencer
Source: http://www.cbs.dtu.dk/dtucourse/cookbooks/dave/Lekt03bkg.html
http://www.hsls.pitt.edu/guides/genetics
More Movies @ HSLS MolBio Videos
http://www.hsls.pitt.edu/molbio/videos
Retrieve promoter
sequence for a gene
Promoter Sequence

Generic Promoter Seq


UCSC Genome Browser
Human Curated Promoter Seq




Biobase TransPro
mPROMDB
CSH TRED
Eukaryotic Promoter Database (EPD)
http://www.hsls.pitt.edu/guides/genetics
Find sequence information for a gene
-genomic
-mRNA
-promoter - intron-exon coordinates
-protein
Resources
UCSC Genome Browser: http://genome.ucsc.edu/
NCBI Entrez Gene: http://www.ncbi.nlm.nih.gov/gene
Link to the video tutorial:
http://media.hsls.pitt.edu/media/clres2705/sequence.swf
http://media.hsls.pitt.edu/media/clres2705/sequence_2.swf
http://www.hsls.pitt.edu/molbio
Fetching Promoters
http://www.hsls.pitt.edu/molbio/videos/play?v=37
Find Promoter Sequence

Retrieve promoter sequence for :

Human : BCL2, EGFR
C. elegans : let-23
Drosophila: son of sevenless
Yeast: fus3

Tips:







Go to UCSC genome browser
Search by gene name
Click on UCSC genes/Wormbase genes/Flybase genes
Click on Genomic sequence
http://www.hsls.pitt.edu/guides/genetics

http://goo.gl/un8UE
http://goo.gl/un8UE
http://goo.gl/3JnmO
BIOBASE TransPro
http://www.hsls.pitt.edu/guides/genetics
Transcription Start Site (TSS)
http://www.hsls.pitt.edu/guides/genetics
Epigenome and
Encyclopedia of DNA
Elements Project
Spatiotemporal gene expression
EGFR
TP53
A movie on regulated transcription
http://vcell.ndsu.edu/animations/regulatedtranscription/index.htm
Epigenetic mechanisms
Source: NCBI
http://www.ncbi.nlm.nih.gov/books/NBK45788/#epi_sci_bkgrd.About_Epigenetics
Genome in 3D
http://www.nature.com/nature/journal/v470/n7333/pdf/470289a.pdf
Chromatin Immuno-Precititation-Seq
(ChIP-Seq)
Epigenetic Markers
Landmark Paper:
http://www.nature.com/ng/journal/v39/n3/full/ng1966.html
Histone Modifications

http://goo.gl/GQ9V8
http://www.hsls.pitt.edu/guides/genetics
Encode Project
http://www.genome.gov/10005107
ENCODE Project
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001046
Encode Cell Types

http://genome.ucsc.edu/ENCODE/cellTypes.
html
Promoter Database

search.HSLS.MolBio

http://search.hsls.pitt.edu/vivisimo/cgi-bin/query-meta?query=promoter+database&inputform=simple&v:sources=OBRCandBioMedCentral&v:project=BioInfoTools&submit=Search
http://www.hsls.pitt.edu/guides/genetics
Promoter Database
Biobase Knowledge Library
Promoter report
http://www.hsls.pitt.edu/guides/genetics
Retrieve experimentally verified promoter sequence of
a gene i.e. EGFR . What transcription factors binding
sites are reported to be present in the gene regulatory
region ?
Resources
Biobase Transpro:
Link to the video tutorial:
http://media.hsls.pitt.edu/media/clres2705/biobase.swf
http://www.hsls.pitt.edu/molbio
What transcription
factors bind to a
promoter sequence?
Find Transcription Factor Binding Sites
Basic Search:

TESS (Transcription Element Search System)
BIOBASE Match

Phylogenetic Footprinting:


ConSite


http://asp.ii.uib.no:8090/cgi-bin/CONSITE/consite
Footer

http://biodev.hgen.pitt.edu/footer_php/Footerv2_0.php
http://www.hsls.pitt.edu/guides/genetics
Transcription Factors (TF)

Database: Transfac-BioBase

https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi

Classification

https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi

Properties
Binding sites
Matrix

https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi


Transcription Factors
Transcription Factor

http://www.cisreg.ca/cgi-bin/tfe/home.pl
Transfac
http://www.hsls.pitt.edu/guides/genetics
Transcription Factor binding sites
Jonathan M. Keith (ed.), Bioinformatics, Volume II: Structure, Function and
Applications, vol. 453, © 2008 Humana Press,
http://www.hsls.pitt.edu/guides/genetics
Information pertaining to a transcription
factor
http://www.hsls.pitt.edu/molbio/videos/play?v=74
Transcription Factors occupancy analysis

Retrieve potential promoter sequence and
predict transcription factors binding sites
present in the promoter region:

http://media.hsls.pitt.edu/media/clres2705/match.swf
http://www.hsls.pitt.edu/guides/genetics
Retrieve potential promoter sequence of a yeast gene,
fus3 and predict transcription factors binding sites
present in the promoter region.
Resources
Biobase Match: https://portal.biobase-international.com/cgi-bin/build_ghptywl/idb/1.0/searchengine/start.cgi
Link to the video tutorial:
http://media.hsls.pitt.edu/media/clres2705/match.swf
http://www.hsls.pitt.edu/molbio
Use Biobase Match program
http://www.hsls.pitt.edu/molbio/videos/play?v=47
Find conserved transcription factor binding
sites
•Footer
•http://biodev.hgen.pitt.edu/footer_php/Footerv2_0.php
•VISTA Tools
•http://genome.lbl.gov/vista/index.shtml
•rVISTA
•http://genome.lbl.gov/vista/rvista/submit.shtml
•Whole Genome rVISTA
•http://genome-test.lbl.gov/cgi-bin/WGRVistaInputCommon.pl
Footer Result Page
http://www.hsls.pitt.edu/guides/genetics
Browsing the ENCODE Data
Sec61g and EGFR

human chr7:54,801,956-55,305,954
EGFR and Sec61g
http://www.hsls.pitt.edu/guides/genetics
EGFR and Sec61g
Role of the Sec61 translocon in EGF receptor trafficking to the nucleus and gene expression.
Liao HJ, Carpenter G.
Mol Biol Cell. 2007 Mar;18(3):1064-72. Epub 2007 Jan 10.
http://www.hsls.pitt.edu/guides/genetics
Convert the human genomic region between genes
sec61g and EGFR into mouse, rat and zebra fish
genomes
Resource
UCSC Genome Browser: http://genome.ucsc.edu/
Link to the video tutorial:
http://media.hsls.pitt.edu/media/clres2705/ucsc_convert.swf
File: UCSC_convert.swf
http://www.hsls.pitt.edu/molbio
UCSC Genome Browser: Navigating a Genomic Region
http://www.hsls.pitt.edu/guides/genetics
UCSC Genome Browser: Navigating a Genomic Region
http://www.hsls.pitt.edu/guides/genetics
UCSC Genome Browser: Navigating a Genomic Region
What transcription factors bind in this region?
http://www.hsls.pitt.edu/guides/genetics
Sec61g and EGFR
Identify promoter, enhancer and silencer sequences by
browsing the epigenomic markers generated by the
ENCODE project
Resource
UCSC Genome Browser: http://genome.ucsc.edu/
Link to the video tutorial:
http://media.hsls.pitt.edu/media/molbiovideos/encode1-ac0212.swf
http://media.hsls.pitt.edu/media/molbiovideos/encode2-ac0212.swf
http://media.hsls.pitt.edu/media/molbiovideos/encode3-ac0212.swf
http://www.hsls.pitt.edu/molbio
Cell Lines

K562

NHLF
Human Epigenome Atlas:
http://www.genboree.org/epigenomeatlas/edaccGridViewerPublic.rhtml
Regulome db Search


rs7216389
rs2853669
Regulome
Retrieve MicroRNA
target genes
MicroRNA
http://www.hsls.pitt.edu/molbio
MicroRNA Biology

http://hstalks.com/main/search_bar.php?s=microRNA&l=252&k=TALK
http://www.hsls.pitt.edu/molbio
•Identify miRNA(s) that have been reported or predicted to interact with
a gene.
•Retrieve target genes of a miRNA
Resources
MiRNA database
•Mirbase: http://www.mirbase.org
Target database
•Mirtarbase: http://mirtarbase.mbc.nctu.edu.tw/
•Targetscan: http://www.targetscan.org/
•Miranda: http://www.microrna.org/
•Pictar: http://pictar.mdc-berlin.de/
Link to the video tutorial:
http://media.hsls.pitt.edu/media/clres2705/mirna.swf
http://www.hsls.pitt.edu/molbio
Result comparison of miRNA prediction algorithms
ExprTarget: An Integrative Approach to Predicting Human MicroRNA Targets
PLOs One http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013534
http://www.hsls.pitt.edu/molbio
Thank you!
Any questions?
Carrie Iwema
[email protected]
412-383-6887
Ansuman Chattopadhyay
[email protected]
412-648-1297
http://www.hsls.pitt.edu/guides/genetics

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