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The
GenMAPP MAPP Archives contain a compilation of
pathways and gene/protein information lists from
broad range of resources. Click on the below or
side links to view detailed descriptions for each
archive. All MAPPs can be downloaded through the
GenMAPP installer from the Data menu within the
GenMAPP application or be viewed as web exports
(see below).
MAPP Statistics
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Species HTML MAPP
Archives
HTML
exports of Contributed and a selected
set of Gene Ontology MAPPs are available for
browsing and gene/protein queries (see Gene
Index). Selected species MAPPs are shown for those
archives containing GenMAPP curated pathway MAPPs,
however, Gene Ontology and KEGG XML converted
MAPPs and MAPPFinder accessible Gene Ontology
categories are available for a number of
additional supported GenMAPP species (see the
online GenMAPP
Help for information on supported
species). Proceed here,
for instructions on downloading actual GenMAPP
Pathway MAPPs.
MAPP
Archive Descriptions
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 fruitfly. To contribute new
MAPPs contact us at: genmapp@gladstone.ucsf.edu |
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Inferred
MAPPs |
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MAPPs
for several species have been inferred from human
MAPPs, using orthology information. These MAPPs
are now available for download for chicken,
dog, worm, yeast,
zebrafish and fruitfly. The MAPP
archives are designated as “Inferred”. 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.
More details on all of the existing MAPP archives
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 at Gladstone/UCSF 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/).
For information on downloading these and
other MAPP archives, proceed here.
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GO-Sample MAPPs |
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The
GenMAPP GO MAPP Archive is a collection of GO
terms formatted as GenMAPP MAPP files. The
collection does not represent the entire GO
hierarchy, but rather the subset of terms
containing more than 100 genes (50 for
C.familiaris) but less than 300 genes.
These
MAPPs were automatically generated by GenMAPP.org.
GO MAPPs are formatted as lists of genes, and do
not contain any graphics other than the gene
object and the label. The MAPPs can be modified in
GenMAPP.
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 MAPP Archive when loading local
MAPPs into MAPPFinder. Since the MAPPFinder
application automatically calculates results based
on the full GO hierarchy, including the GO MAPP
Archives is redundant and will result in delays
and potential problems when running
MAPPFinder.
Available
for all supported species. |
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SGD-metabolic MAPPs |
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These pathways
were derived from the yeast pathways at SGD, http://pathway.yeastgenome.org/biocyc/.
Available
for yeast. |
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KEGG converted MAPPs |
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The
KEGG Converted MAPPs were converted from the
Pathway Resource at the Kyoto Encyclopedia of
Genes and Genomes at http://www.genome.ad.jp/kegg/.
The
KEGG MAPPs were converted from the XML files
representing the KEGG
Metabolic Maps KGML 2.0,
at ftp://ftp.genome.ad.jp/pub/kegg/
. The XML representation provided by KEGG does not
always completely match the graphic display of
pathways shown at the KEGG site. This is
particularly true for relationships between
objects which are frequently not fully represented
in the XML. The result is that the GenMAPP
converted MAPPs may look somewhat different from
the KEGG site HTML maps.
Where applicable, the
KEGG EC number for enzymes has been converted to
one
or more gene accession numbers based on
conversion data provided by KEGG. No gene ID
has been provided for those genes which retain the
EC number designation (instead of a gene name) on
a GenMAPP MAPP for that particular
species.
Available
for yeast, fruitfly, zebrafish and worm. Available
for human, mouse, rat and yeast by request
only. |
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