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Document related concepts
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Transcript 
Genomic Databases
Cédric Notredame
Cédric Notredame (23/05/2017)
Databases
The Next Generation
Cédric Notredame
Cédric Notredame (23/05/2017)
HOT !!!
VERY HOT !!!
Cédric Notredame (23/05/2017)
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
Gene Ontology:
Words to describe all this
Cédric Notredame (23/05/2017)
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 (23/05/2017)
Gory Details
What is inside the resource
Biological Questions
You Can Ask
Alternative Ressources
Cédric Notredame (23/05/2017)
Watch Out!
Cédric Notredame (23/05/2017)
ENSEMBL:
Where is my Gene in
the Human Genome
(who are its neighbors)
?
Cédric Notredame (23/05/2017)
Using ENSEMBL
www.ensembl.org
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
What are the Neighbours of the DUT Gene
In the Human Genome ?
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
What are the genes, on chromosome 1, that have been
linked to a disease, and for which SNPs
(Single Nucleotide Polymorphisms) have been identified?
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
Select a Chromosome
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
Select your filter
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
Select The
Information
You Need
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
Cédric Notredame (23/05/2017)
Using ENSEMBL: Asking a question
Cédric Notredame (23/05/2017)
ENSEMBL Questions
What are the Neighbours of the DUT Gene
In the Human Genome ?
What are the genes, on chromosome 1, that have been
linked to a disease, and for which SNPs
(Single Nucleotide Polymorphisms) have been identified?
Cédric Notredame (23/05/2017)
ENSEMBL: Watch Out
Your Transcript of Interest May not be mapped
Use Sim4
All the potential alternative splice forms are
not always mapped
Exons may be lost
Cédric Notredame (23/05/2017)
ENSEMBL:
A Few Alternative Resources
www.ncbi.nlm.nih.gov
NCBI
genome.ucsc.edu
UCSC
www.genome.ad.jp
Cédric Notredame (23/05/2017)
GenomeNet
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
Gene Ontology:
Words to describe all this
Cédric Notredame (23/05/2017)
TRANSFAC:
Who Turns On My
Gene
?
Cédric Notredame (23/05/2017)
TRANSFAC
Introducing TRANSFAC
Cédric Notredame (23/05/2017)
www.gene-regulation.com
Cédric Notredame (23/05/2017)
Using TRANSFAC
What are the transcription Factor Classes
that contain a Zinc Finger
Cédric Notredame (23/05/2017)
Select a Class
Cédric Notredame (23/05/2017)
Keyword
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Using TRANSFAC
What is Known about the ACE2
Transcription Factor
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Using TRANSFAC
What is The Specificity of my Factor
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
TRANSFAC:
A Few Related Resources
www.epd.isb-sib.ch
Cédric Notredame (23/05/2017)
TRANSFAC:
A Few Alternative Resources
prodoric.tu-bs.de
www.cbrc.jp/research/db/TFSEARCH.html
Cédric Notredame (23/05/2017)
PRODORIC
GenomeNet
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
Gene Ontology:
Words to describe all this
Cédric Notredame (23/05/2017)
KEGG:
Where Does My
Protein Work
?
Cédric Notredame (23/05/2017)
KEGG
Introducing KEGG
Cédric Notredame (23/05/2017)
www.genome.ad.jp/kegg/
Cédric Notredame (23/05/2017)
2003
2004
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
KEGG
How Does it Work ?
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Link DB Meta-Database/Search Engine
PATHWAY
KO
Genes
Cédric Notredame (23/05/2017)
Reference Pathways
Kegg Orthology
Compiled Gene List
Cédric Notredame (23/05/2017)
Using KEGG
What are the Enzymes involved in the Glycolysis
in Homo Sapiens
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Using KEGG
What are the Homo Sapiens
RNA polymerase made of
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Using KEGG
How can a cell turn Glycine into Alanine
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Connecting Enzymes
that may not Co-Exist…
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Using KEGG
Some other things you can do with KEGG
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
KEGG
Glycolysis in Homo Sapiens
RNA polymerase in Homo Sapiens
Turning a Glycine into Alanine
Cédric Notredame (23/05/2017)
COG:
KEGG Alternative ???
www.ncbi.nlm.nih.gov/COG/
Cédric Notredame (23/05/2017)
NCBI COGs
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
Gene Ontology:
Words to describe all this
Cédric Notredame (23/05/2017)
DIP and BIND:
Who Does My Protein
Interact With
?
Cédric Notredame (23/05/2017)
BIND
Introducing BIND
Cédric Notredame (23/05/2017)
www.blueprint.org
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Using BIND
What are the known complexes involving
the CDK1 Kinase
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
DIP
Introducing DIP
Cédric Notredame (23/05/2017)
dip.doe-mbi.ucla.edu
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Using DIP
What are the known complexes involving
the CDK1 Kinase
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Using DIP
What are the potential Interactions
between my Genes:
Can I make an Educated Guess
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Not Very Reliable:
False Negatives
False Positives
Cédric Notredame (23/05/2017)
DIP, BIND:
A Few Alternative Resources
Cédric Notredame (23/05/2017)
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
Gene Ontology:
Words to describe all this
Cédric Notredame (23/05/2017)
GeneCard:
What is Known About
my Gene ?
Cédric Notredame (23/05/2017)
GeneCard
Introducing GENECARD
Cédric Notredame (23/05/2017)
www.genecards.ac.il
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
« Scientists Would Rather
Share their Toothbrush than
their Gene Names… »
Michael Ashburner
Cédric Notredame (23/05/2017)
GeneCard
How Does it Work ?
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Asking a question with GENECARD
What is The GeneCard of the BRCA1 gene ?
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Asking a question with GENECARD
What is there to find about p53 in GeneCard
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Asking a question with GENECARD
I want to find out about Apoptosis
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Asking a question with GENECARD
Some Tips on Making the right Request
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
Gene Ontology:
Words to describe all this
Cédric Notredame (23/05/2017)
Gene Ontology:
Describing Your Gene
With the Right
Words
Cédric Notredame (23/05/2017)
Using GO
What is this “Tubulin Binding function”
indicated within
The BRCA1 GeneCaRD
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Asking a question with AMIGO
How can I describe the CDK1 according to
the Gene Ontology
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
mor.nlm.nih.gov/perl/gennav.pl
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Gene Ontology
Who Runs it ?
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
KEGG
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Gene Ontology
Relating GO to other systems
Cédric Notredame (23/05/2017)
KO2GO ???
COG2GO ???
Cédric Notredame (23/05/2017)
SP
<->
GO
EC <->GO
Cédric Notredame (23/05/2017)
www.geneontology.org/GO.current.annotations.shtml
Cédric Notredame (23/05/2017)
Cédric Notredame (23/05/2017)
Genomic Databases
A Summary
Cédric Notredame (23/05/2017)
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
What are the Neighbours
of the DUT Gene
Gene Ontology:
In
the to
Human
Genome
Words
describe
all this?
Cédric Notredame (23/05/2017)
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
What is Known about the ACE2
Gene Ontology:
Transcription
Factor
Words to describe all this
Cédric Notredame (23/05/2017)
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
Glycolysis in Homo Sapiens
Gene Ontology:
Turning a Glycine
into Alanine
Words to describe all this
Cédric Notredame (23/05/2017)
ENSEMBL
TRANSFAC
KEGG
GENECARD
DIP, BIND
Who Does Interact
With My Protein?
Gene Ontology:
Words to describe all this
Cédric Notredame (23/05/2017)
ENSEMBL
I Want A summary of
Everything known about TRANSFAC
my
Protein
KEGG
GENECARD
DIP, BIND
Gene Ontology:
Words to describe all this
Cédric Notredame (23/05/2017)
ENSEMBL
I Want A summary of
Everything known about TRANSFAC
my
Protein
KEGG
GENECARD
DIP, BIND
What Is the Meaning
Of the Words describing
My Protein
Gene Ontology:
Words to describe all this
Cédric Notredame (23/05/2017)
These Resources Rely a LOT
on automated procedures
They Are FULL of errors
They Make an ideal starting
point But…
DOUBLE CHECK
IMPORTANT ASSERTIONS
Cédric Notredame (23/05/2017)
A few Links
Cédric Notredame (23/05/2017)
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
Cédric Notredame (23/05/2017)
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