Transcript Exploring the Human Genome - Cayetano Heredia University

NCBI
Virus: Genomas completos
NCBI
Bacterias: Genomas completos
NCBI
Oganelas: Genomas completos
Exploring the
Human Genome
ENSEMBL
Que es ENSEMBL
–EMBL – European Bioinformatics
Institute (EBI)
–Wellcome Trust Sanger Institute
PAGINA PRINCIPAL
Pre! and Archive! sites
http://pre.ensembl.org
http://www.ensembl.org
http://archive.ensembl.org
PAGINA PRINCIPAL
UN BUEN EJEMPLO
PAGINA PRINCIPAL
Proyecto Genoma Humano
CONTIG VIEWS
FEATURES
DAS
CytoView
Family
View
Ensembl – Open source
BIOMART
DATA MINING
BioMart
Query:
• For all mouse genes on chromosome 10 that
are protein coding, I would like to know the
IDs in both Ensembl and MGI.
• In the query:
Attributes: what we want to know.
Filters: what we know
Query:
• For all mouse genes on chromosome 10 that
are protein coding, I would like to know the
IDs in both Ensembl and MGI.
• In the query:
Attributes: what we want to know.
Filters: what we know
Query:
• For all mouse genes on chromosome 10 that
are protein coding, I would like to know the
IDs in both Ensembl and MGI.
• In the query:
Attributes: what we want to know.
Filters: what we know
A Brief Example
Change dataset to
mouse
Mus musculus
A Brief Example
Dataset has changed.
Attributes (Output Options)
Click
Attributes.
Click on ‘GENE’.
Attributes allow us to choose what we wish to
know.
IDs are found in the ‘Features’ page.
Attributes (Output Options)
Ensembl Gene ID is
selected
Default options selected:
Ensembl Gene ID and Transcript ID
Attributes (Output Options)
‘Markersymbol ID’ will
give us the MGI ID
Scroll down to select MGI symbol.
Also select the accession number.
The Results Table
‘Results’ give us Gene IDs for all mouse genes in
the Ensembl database.
Select a Smaller Gene Set
Expand the
REGION panel
Select
‘Filters’
Instead of all mouse genes, select protein coding
genes on chromosome 10.
Select Genes on Chromosome 10
Select
chromosome
10
Instead of all mouse genes, select protein coding
genes on chromosome 10.
Select Protein Coding Genes
Gene type:
protein coding
Filters are set to chromosome 10 and
protein-coding genes. Genes must meet BOTH
criteria to be in the result table.
Results (Preview)
For the full result
table: Go
This is a preview- if you are happy with the table,
click ‘Go’.
Full Result Table
Ensembl Gene ID
Transcript
ID
MGI
symbol
MGI Accession
Number
Original Query:
• For all mouse genes on chromosome
10 that are protein coding, I would like
to know the IDs in both Ensembl and
MGI.
• In the query:
Attributes: columns in the Result Table
Filters: what we know
THE UCSC GENOME
BIOINFORMATICS
Otras herramientas para la búsqueda
TIGR
The Institute for Genomic Research
www.tigr.org/tdb/