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GenMAPP MAPP Archives
The
GenMAPP MAPP Archives contain
pathways and gene/protein lists from
broad range of resources. Click on the below links to view detailed descriptions for each
archive. All MAPPs can be downloaded through the
GenMAPP Data Acquisition tool within the GenMAPP
application.
GenMAPP pathways can also be browsed at
WikiPathways
MAPP Statistics
Oct 4, 2007
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MAPP
Archives
Contributed
MAPPs
The
GenMAPP.org MAPPs is a collection of hand-curated
pathways created at GenMAPP.org or submitted to us
by GenMAPP users. Each MAPP contains contact
information for the author. Available for human,
mouse, rat, yeast and fruit fly. To contribute new
MAPPs contact us at: genmapp@gladstone.ucsf.edu |
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Converted MAPPs |
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MAPPs
for several species have been converted from human MAPPs, using orthology
information. Human was
chosen as the template species for conversion and ortholog information between human and the
applicable target species was obtained from Homologene
and from Ensembl. The
data utilized from these resources was restricted
to the one-to-one gene relationships between
template and target species. Conversion between
species was accomplished using the Converter tool
in GenMAPP. MAPPs were 50% or more of the genes
converted between species were included in the
archive.
A
descriptive manual for how to convert MAPPs
between species is available
here. |
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Tissue-Specific
MAPPs |
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The
tissue-specific MAPP archive was developed in the
Conklin
Lab in close collaboration
with Jonathan Schug in the Stoeckert
lab at the University of Pennsylvania Center
for Bioinformatics. The primary purpose of these
MAPPs is to allow researchers to identify tissue
specific gene expression patterns in DNA microarray data. The determination of tissue
specific genes was based on the analysis of two
microarray datasets generated by the Genomic
Institute of the Novartis Foundation (PNAS
2004 Apr 20;101(16):6062-7 and PNAS 2002 Apr
2;99(7):4465-70; http://symatlas.gnf.org/SymAtlas/).
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GO Sample MAPPs |
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The
GenMAPP GO Sample MAPP Archive is a collection of GO
terms automatically generated by GenMAPP.org and formatted as GenMAPP MAPP files. The
collection does not represent the entire GO
hierarchy, but rather the subset of terms
containing between 100 (50 for
C.familiaris) and 300 genes. GO MAPPs are formatted as lists of genes, and do
not contain any graphics other than the gene
object and the label.
The
purpose of the GO MAPPs is to make the GO terms
available outside the MAPPFinder application. The
GO MAPPs serve as a starting point for creating
annotated MAPPs for areas of biology not covered
by the curated MAPP Archives.NOTE: Do
not include the GO Sample MAPP Archive when loading local
MAPPs in MAPPFinder. MAPPFinder automatically calculates results based
on the full GO hierarchy, so including the GO MAPP
Archives is redundant and will result in delays
and potential problems when running
MAPPFinder. |
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SGD-metabolic MAPPs |
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These pathways
were derived from the yeast pathways at
SGD.
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KEGG converted MAPPs |
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The
KEGG Converted MAPPs were automatically converted
from the XML files available
from the Pathway Resource at the
Kyoto
Encyclopedia of Genes and Genomes.
GenMAPP
converted KEGG MAPPs may look somewhat different from
the KEGG site HTML maps since
the XML representation provided by KEGG does not
always completely match the graphic display of
pathways shown at the KEGG site. Where applicable, the
KEGG EC number for enzymes has been converted to
one or more gene IDs based on
conversion data provided by KEGG.
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GenMAPP Gene Databases
The
GenMAPP Gene Databases are species-specific collections
of genes and annotation. Click on the links below
for details and graphs on Gene Database content.
All Gene Databases can be downloaded using the
Data Acquisition tool in GenMAPP.
Figure 1: Gene ID systems
represented in current Gene Databases (Oct 4,
2007)
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Human |
Mouse |
Rat |
Dog |
Cattle |
Chicken |
Yeast |
Zebrafish |
Fruit
fly |
Mosquito |
Worm |
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Ensembl |
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Entrez
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UniProt |
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Unigene |
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RefSeq
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Affymetrix |
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Agilent |
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Illumina |
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Codelink |
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MGI |
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HUGO |
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RGD |
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SGD |
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ZFIN |
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FlyBase |
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WormBase |
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PDB |
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GeneOntology |
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Pfam |
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OMIM |
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InterPro |
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EMBL |
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