Genomic Databases Cdric Notredame 28102020 Databases The Next

Genomic Databases Cédric Notredame (28/10/2020)

Databases The Next Generation Cédric Notredame (28/10/2020)

HOT !!! VERY HOT !!! Cédric Notredame (28/10/2020)

ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND Gene Ontology: Words to describe all this Cédric Notredame (28/10/2020)

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 (28/10/2020)

Gory Details What is inside the resource Biological Questions You Can Ask Alternative Ressources Cédric Notredame (28/10/2020)

Watch Out! Cédric Notredame (28/10/2020)

ENSEMBL: Where is my Gene in the Human Genome (who are its neighbors) ? Cédric Notredame (28/10/2020)

Using ENSEMBL www. ensembl. org Cédric Notredame (28/10/2020)

Using ENSEMBL: Asking a question What are the Neighbours of the DUT Gene In the Human Genome ? Cédric Notredame (28/10/2020)

Using ENSEMBL: Asking a question Cédric Notredame (28/10/2020)

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 (28/10/2020)

Using ENSEMBL: Asking a question Cédric Notredame (28/10/2020)

Using ENSEMBL: Asking a question Select a Chromosome Cédric Notredame (28/10/2020)

Using ENSEMBL: Asking a question Select your filter Cédric Notredame (28/10/2020)

Using ENSEMBL: Asking a question Select The Information You Need Cédric Notredame (28/10/2020)

Using ENSEMBL: Asking a question Cédric Notredame (28/10/2020)

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 (28/10/2020)

ENSEMBL: Watch Out Your Transcript of Interest May not be mapped Use Sim 4 All the potential alternative splice forms are not always mapped Exons may be lost Cédric Notredame (28/10/2020)

ENSEMBL: A Few Alternative Resources www. ncbi. nlm. nih. gov genome. ucsc. edu www. genome. ad. jp Cédric Notredame (28/10/2020) NCBI UCSC Genome. Net

ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND Gene Ontology: Words to describe all this Cédric Notredame (28/10/2020)

TRANSFAC: Who Turns On My Gene ? Cédric Notredame (28/10/2020)

TRANSFAC Introducing TRANSFAC Cédric Notredame (28/10/2020)

www. gene-regulation. com Cédric Notredame (28/10/2020)

Using TRANSFAC What are the transcription Factor Classes that contain a Zinc Finger Cédric Notredame (28/10/2020)

Select a Class Cédric Notredame (28/10/2020)

Keyword Cédric Notredame (28/10/2020)

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Using TRANSFAC What is Known about the ACE 2 Transcription Factor Cédric Notredame (28/10/2020)

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Using TRANSFAC What is The Specificity of my Factor Cédric Notredame (28/10/2020)

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TRANSFAC: A Few Related Resources www. epd. isb-sib. ch Cédric Notredame (28/10/2020)

TRANSFAC: A Few Alternative Resources prodoric. tu-bs. de www. cbrc. jp/research/db/TFSEARCH. html Cédric Notredame (28/10/2020) PRODORIC Genome. Net

ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND Gene Ontology: Words to describe all this Cédric Notredame (28/10/2020)

KEGG: Where Does My Protein Work ? Cédric Notredame (28/10/2020)

KEGG Introducing KEGG Cédric Notredame (28/10/2020)

www. genome. ad. jp/kegg/ Cédric Notredame (28/10/2020)

2003 2004 Cédric Notredame (28/10/2020)

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KEGG How Does it Work ? Cédric Notredame (28/10/2020)

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Link DB Meta-Database/Search Engine PATHWAY KO Genes Cédric Notredame (28/10/2020) Reference Pathways Kegg Orthology Compiled Gene List

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Using KEGG What are the Enzymes involved in the Glycolysis in Homo Sapiens Cédric Notredame (28/10/2020)

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Using KEGG What are the Homo Sapiens RNA polymerase made of Cédric Notredame (28/10/2020)

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Using KEGG How can a cell turn Glycine into Alanine Cédric Notredame (28/10/2020)

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Connecting Enzymes that may not Co-Exist… Cédric Notredame (28/10/2020)

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Using KEGG Some other things you can do with KEGG Cédric Notredame (28/10/2020)

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KEGG Glycolysis in Homo Sapiens RNA polymerase in Homo Sapiens Turning a Glycine into Alanine Cédric Notredame (28/10/2020)

COG: KEGG Alternative ? ? ? www. ncbi. nlm. nih. gov/COG/ Cédric Notredame (28/10/2020) NCBI COGs

ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND Gene Ontology: Words to describe all this Cédric Notredame (28/10/2020)

DIP and BIND: Who Does My Protein Interact With ? Cédric Notredame (28/10/2020)

BIND Introducing BIND Cédric Notredame (28/10/2020)

www. blueprint. org Cédric Notredame (28/10/2020)

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Using BIND What are the known complexes involving the CDK 1 Kinase Cédric Notredame (28/10/2020)

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DIP Introducing DIP Cédric Notredame (28/10/2020)

dip. doe-mbi. ucla. edu Cédric Notredame (28/10/2020)

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Using DIP What are the known complexes involving the CDK 1 Kinase Cédric Notredame (28/10/2020)

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Using DIP What are the potential Interactions between my Genes: Can I make an Educated Guess Cédric Notredame (28/10/2020)

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Not Very Reliable: False Negatives False Positives Cédric Notredame (28/10/2020)

DIP, BIND: A Few Alternative Resources Cédric Notredame (28/10/2020)

ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND Gene Ontology: Words to describe all this Cédric Notredame (28/10/2020)

Gene. Card: What is Known About my Gene ? Cédric Notredame (28/10/2020)

Gene. Card Introducing GENECARD Cédric Notredame (28/10/2020)

www. genecards. ac. il Cédric Notredame (28/10/2020)

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« Scientists Would Rather Share their Toothbrush than their Gene Names… » Michael Ashburner Cédric Notredame (28/10/2020)

Gene. Card How Does it Work ? Cédric Notredame (28/10/2020)

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Asking a question with GENECARD What is The Gene. Card of the BRCA 1 gene ? Cédric Notredame (28/10/2020)

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Asking a question with GENECARD What is there to find about p 53 in. Gene. Card Cédric Notredame (28/10/2020)

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Asking a question with GENECARD I want to find out about Apoptosis Cédric Notredame (28/10/2020)

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Asking a question with GENECARD Some Tips on Making the right Request Cédric Notredame (28/10/2020)

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ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND Gene Ontology: Words to describe all this Cédric Notredame (28/10/2020)

Gene Ontology: Describing Your Gene With the Right Words Cédric Notredame (28/10/2020)

Using GO What is this “Tubulin Binding function” indicated within The BRCA 1 Gene. Ca. RD Cédric Notredame (28/10/2020)

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Asking a question with AMIGO How can I describe the CDK 1 according to the Gene Ontology Cédric Notredame (28/10/2020)

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mor. nlm. nih. gov/perl/gennav. pl Cédric Notredame (28/10/2020)

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Gene Ontology Who Runs it ? Cédric Notredame (28/10/2020)

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KEGG Cédric Notredame (28/10/2020)

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Gene Ontology Relating GO to other systems Cédric Notredame (28/10/2020)

KO 2 GO ? ? ? COG 2 GO ? ? ? Cédric Notredame (28/10/2020)

SP <-> GO EC <->GO Cédric Notredame (28/10/2020)

www. geneontology. org/GO. current. annotations. shtml Cédric Notredame (28/10/2020)

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Genomic Databases A Summary Cédric Notredame (28/10/2020)

ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND What are the Neighbours of the DUT Gene Ontology: In the to Human Genome Words describe all this? Cédric Notredame (28/10/2020)

ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND What is Known about the ACE 2 Gene Ontology: Transcription Factor Words to describe all this Cédric Notredame (28/10/2020)

ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND Glycolysis in Homo Sapiens Gene Ontology: Turning a Glycine into Alanine Words to describe all this Cédric Notredame (28/10/2020)

ENSEMBL TRANSFAC KEGG GENECARD DIP, BIND Who Does Interact With My Protein? Gene Ontology: Words to describe all this Cédric Notredame (28/10/2020)

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 (28/10/2020)

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 (28/10/2020)

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 (28/10/2020)

A few Links Cédric Notredame (28/10/2020)

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 Gen. Cards www. geneontology. org G. Ontology Cédric Notredame (28/10/2020)