UCSC Genome Browser - University of Pittsburgh
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Transcript UCSC Genome Browser - University of Pittsburgh
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