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Cédric Notredame (18/06/22) Genomic Databases Cédric Notredame
Cédric Notredame (21/04/23)
Genomic Databases
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Cédric Notredame
Databases The Next Generation
Cédric Notredame (21/04/23)
HOT !!!
VERY HOT !!!
Cédric Notredame (21/04/23)
ENSEMBL
KEGG
DIP, BIND
TRANSFAC
GENECARD
Gene Ontology: Words to describe all this
Cédric Notredame (21/04/23)
ANNOTATION
-Where are the genes ?
-What do they do: Biochemistry ?
-When do they do it: Regulation ?
-Who do they do it for: Metabolic ?
Cédric Notredame (21/04/23)
What is inside the resource
Gory Details
Biological Questions You Can Ask
Alternative Ressources
Cédric Notredame (21/04/23)
Watch Out!
Cédric Notredame (21/04/23)
ENSEMBL:
Where is my Gene in the Human
Genome (who are its neighbors) ?
Cédric Notredame (21/04/23)
Using ENSEMBL
www.ensembl.org
Cédric Notredame (21/04/23)
What are the Neighbours of the DUT GeneIn the Human Genome ?
Using ENSEMBL: Asking a question
Cédric Notredame (21/04/23)
Using ENSEMBL: Asking a question
Cédric Notredame (21/04/23)
Using ENSEMBL: Asking a question
Cédric Notredame (21/04/23)
Using ENSEMBL: Asking a question
What are the genes, on chromosome 1, that have beenlinked to a disease, and for which SNPs (Single Nucleotide Polymorphisms) have been identified?
Cédric Notredame (21/04/23)
Using ENSEMBL: Asking a question
Cédric Notredame (21/04/23)
Using ENSEMBL: Asking a question
Select a Chromosome
Cédric Notredame (21/04/23)
Using ENSEMBL: Asking a question
Select your filter
Cédric Notredame (21/04/23)
Using ENSEMBL: Asking a question
Select The Information You Need
Cédric Notredame (21/04/23)
Using ENSEMBL: Asking a question
Cédric Notredame (21/04/23)
Using ENSEMBL: Asking a question
Cédric Notredame (21/04/23)
What are the Neighbours of the DUT GeneIn the Human Genome ?
ENSEMBL Questions
What are the genes, on chromosome 1, that have beenlinked to a disease, and for which SNPs (Single Nucleotide Polymorphisms) have been identified?
Cédric Notredame (21/04/23)
Your Transcript of Interest May not be mapped
Use Sim4
ENSEMBL: Watch Out
All the potential alternative splice forms are not always mapped
Exons may be lost
Cédric Notredame (21/04/23)
ENSEMBL: A Few Alternative Resources
www.ncbi.nlm.nih.gov NCBI
genome.ucsc.edu UCSC
www.genome.ad.jp GenomeNet
Cédric Notredame (21/04/23)
GENECARD
KEGG
DIP, BIND
Gene Ontology: Words to describe all this
ENSEMBL
TRANSFAC
Cédric Notredame (21/04/23)
TRANSFAC:
Who Turns On My Gene
?
Cédric Notredame (21/04/23)
Introducing TRANSFAC
TRANSFAC
Cédric Notredame (21/04/23)
www.gene-regulation.com
Cédric Notredame (21/04/23)
What are the transcription Factor Classes that contain a Zinc Finger
Using TRANSFAC
Cédric Notredame (21/04/23)
Select a Class
Cédric Notredame (21/04/23)
Keyword
Cédric Notredame (21/04/23)
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What is Known about the ACE2Transcription Factor
Using TRANSFAC
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
What is The Specificity of my Factor
Using TRANSFAC
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
www.epd.isb-sib.ch
TRANSFAC: A Few Related Resources
Cédric Notredame (21/04/23)
TRANSFAC: A Few Alternative Resources
prodoric.tu-bs.de PRODORIC
www.cbrc.jp/research/db/TFSEARCH.html
GenomeNet
Cédric Notredame (21/04/23)
ENSEMBL
GENECARD DIP, BIND
Gene Ontology: Words to describe all this
TRANSFAC
KEGG
Cédric Notredame (21/04/23)
KEGG:
Where Does My Protein Work
?
Cédric Notredame (21/04/23)
Introducing KEGG
KEGG
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www.genome.ad.jp/kegg/
Cédric Notredame (21/04/23)
2003
2004
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Cédric Notredame (21/04/23)
How Does it Work ?
KEGG
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
PATHWAY Reference PathwaysKO Kegg OrthologyGenes Compiled Gene List
Link DB Meta-Database/Search Engine
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
What are the Enzymes involved in the Glycolysis in Homo Sapiens
Using KEGG
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
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Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
What are the Homo Sapiens RNA polymerase made of
Using KEGG
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
How can a cell turn Glycine into Alanine
Using KEGG
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Connecting Enzymes that may not Co-Exist…
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Some other things you can do with KEGG
Using KEGG
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Glycolysis in Homo Sapiens
KEGG
RNA polymerase in Homo Sapiens
Turning a Glycine into Alanine
Cédric Notredame (21/04/23)
COG: KEGG Alternative ???
www.ncbi.nlm.nih.gov/COG/ NCBI COGs
Cédric Notredame (21/04/23)
ENSEMBL
TRANSFAC
GENECARD
Gene Ontology: Words to describe all this
KEGG
DIP, BIND
Cédric Notredame (21/04/23)
DIP and BIND:
Who Does My Protein Interact
With?
Cédric Notredame (21/04/23)
Introducing BIND
BIND
Cédric Notredame (21/04/23)
www.blueprint.org
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
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Cédric Notredame (21/04/23)
What are the known complexes involving the CDK1 Kinase
Using BIND
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
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Cédric Notredame (21/04/23)
Introducing DIP
DIP
Cédric Notredame (21/04/23)
dip.doe-mbi.ucla.edu
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
What are the known complexes involving the CDK1 Kinase
Using DIP
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What are the potential Interactions between my Genes:
Can I make an Educated Guess
Using DIP
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Not Very Reliable:
False Negatives
False Positives
Cédric Notredame (21/04/23)
DIP, BIND: A Few Alternative Resources
Cédric Notredame (21/04/23)
DIP, BIND
KEGG
ENSEMBL
TRANSFAC
Gene Ontology: Words to describe all this
GENECARD
Cédric Notredame (21/04/23)
GeneCard:
What is Known About my Gene ?
Cédric Notredame (21/04/23)
Introducing GENECARD
GeneCard
Cédric Notredame (21/04/23)
www.genecards.ac.il
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
« Scientists Would Rather Share their Toothbrush than their Gene Names… »
Michael Ashburner
Cédric Notredame (21/04/23)
How Does it Work ?
GeneCard
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
What is The GeneCard of the BRCA1 gene ?
Asking a question with GENECARD
Cédric Notredame (21/04/23)
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What is there to find about p53 in GeneCard
Asking a question with GENECARD
Cédric Notredame (21/04/23)
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Cédric Notredame (21/04/23)
I want to find out about Apoptosis
Asking a question with GENECARD
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Some Tips on Making the right Request
Asking a question with GENECARD
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
DIP, BIND
KEGG
ENSEMBL
TRANSFAC
GENECARD
Gene Ontology: Words to describe all this
Cédric Notredame (21/04/23)
Gene Ontology:
Describing Your Gene
With the Right Words
Cédric Notredame (21/04/23)
What is this “Tubulin Binding function” indicated within
The BRCA1 GeneCaRD
Using GO
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
How can I describe the CDK1 according to the Gene Ontology
Asking a question with AMIGO
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
mor.nlm.nih.gov/perl/gennav.pl
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Who Runs it ?
Gene Ontology
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
KEGG
Cédric Notredame (21/04/23)
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Relating GO to other systems
Gene Ontology
Cédric Notredame (21/04/23)
KO2GO ???COG2GO ???
Cédric Notredame (21/04/23)
EC <->GO
SP <->GO
Cédric Notredame (21/04/23)
www.geneontology.org/GO.current.annotations.shtml
Cédric Notredame (21/04/23)
Cédric Notredame (21/04/23)
Genomic Databases
A Summary
Cédric Notredame (21/04/23)
DIP, BIND
KEGG
TRANSFAC
GENECARD
Gene Ontology: Words to describe all this
ENSEMBL
What are the Neighbours of the DUT GeneIn the Human Genome ?
Cédric Notredame (21/04/23)
ENSEMBL
DIP, BIND
KEGG
GENECARD
Gene Ontology: Words to describe all this
What is Known about the ACE2Transcription Factor
TRANSFAC
Cédric Notredame (21/04/23)
TRANSFAC
ENSEMBL
DIP, BINDGENECARD
Gene Ontology: Words to describe all this
KEGG
Glycolysis in Homo Sapiens
Turning a Glycine into Alanine
Cédric Notredame (21/04/23)
TRANSFAC
ENSEMBL
KEGG
GENECARD
Gene Ontology: Words to describe all this
Who Does Interact With My Protein?
DIP, BIND
Cédric Notredame (21/04/23)
DIP, BIND
TRANSFAC
ENSEMBL
KEGG
Gene Ontology: Words to describe all this
I Want A summary of Everything known about my
Protein
GENECARD
Cédric Notredame (21/04/23)
DIP, BIND
TRANSFAC
ENSEMBL
KEGG
I Want A summary of Everything known about my
Protein
GENECARD
Gene Ontology: Words to describe all this
What Is the MeaningOf the Words describing
My Protein
Cédric Notredame (21/04/23)
These Resources Rely a LOT on automated proceduresThey Are FULL of errors
They Make an ideal starting point But…
DOUBLE CHECK
IMPORTANT ASSERTIONS
Cédric Notredame (21/04/23)
A few Links
Cédric Notredame (21/04/23)
www.ensembl.org ENSEMBL
www.gene-regulation.com TRANSFAC
www.epd.isb-sib.ch EPD
www.genome.ad.jp/kegg/ KEGG
www.blueprint.org BIND
dip.doe-mbi.ucla.edu DIP
www.genecards.ac.il GenCards
www.geneontology.org G. Ontology
