PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
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References
35,225 citations
"PANTHER version 7: improved phyloge..." refers background in this paper
...Gene function—or, more commonly, the function of gene products such as proteins—is described using terms from the Gene ontology (GO) (3,4), or from representations of molecular pathways....
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4,074 citations
"PANTHER version 7: improved phyloge..." refers background or methods in this paper
...Arabidopsis thaliana ARATH TAIR (11) Dicot plant Caenorhabditis elegans CAEEL WormBase (12) Nematode worm Danio rerio DANRE Ensembl, ZFIN (13) Zebrafish Dictyostelium discoideum DICDI DictyBase (14) Cellular slime mold Drosophila melanogaster DROME FlyBase (15) Fruit fly Escherichia coli ECOLI EcoCyc (16) Bacterium Gallus gallus CHICK Entrez Gene (17) Chicken Homo sapiens HUMAN SwissProt (18) Human Mus musculus MOUSE MGI (19) Mouse Rattus norvegicus RAT RGD (20) Rat Saccharomyces cerevisiae YEAST SGD (21) Budding yeast Schizosaccharomyces pombe SCHPO GeneDB (22) Fission yeast Other chordate genomes Ensembl (23) Other non-chordate genomes Entrez Gene (17) Nucleic Acids Research, 2010, Vol....
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...In PANTHER 7, we now also support identifiers from Ensembl (23), model organism databases, the International Protein Index (IPI) (25) and UniProt (18)....
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...All of these identifiers are obtained through the mapping files provided by UniProt (ftp://ftp.uniprot.org/pub/databases/uniprot/ current_release/knowledgebase/idmapping/)....
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3,278 citations
"PANTHER version 7: improved phyloge..." refers methods in this paper
...A multiple sequence alignment was constructed for each family using the MAFFT program (6) and a phylogenetic tree was estimated from the protein multiple alignment....
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2,857 citations
"PANTHER version 7: improved phyloge..." refers background or methods in this paper
...relevant sequences in the MAFFT alignment, trimmed it to include as match states only those columns aligned by 30% of the sequences in the subalignment [sequences were weighted using the same technique as in (1)], and used it to construct an initial model using the modelfromalign program in SAM3....
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...As a result, in PANTHER 7, all molecular function, biological process and cellular component terms are exclusively GO terms [previous versions of PANTHER used the PANTHER/X ontology (1), though a mapping file to GO was provided]....
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...PANTHER (Protein ANalysis THrough Evolutionary Relationships) is a database of phylogenetic trees of protein-coding gene families from all kingdoms of life (1)....
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2,158 citations
"PANTHER version 7: improved phyloge..." refers background in this paper
...Arabidopsis thaliana ARATH TAIR (11) Dicot plant Caenorhabditis elegans CAEEL WormBase (12) Nematode worm Danio rerio DANRE Ensembl, ZFIN (13) Zebrafish Dictyostelium discoideum DICDI DictyBase (14) Cellular slime mold Drosophila melanogaster DROME FlyBase (15) Fruit fly Escherichia coli ECOLI EcoCyc (16) Bacterium Gallus gallus CHICK Entrez Gene (17) Chicken Homo sapiens HUMAN SwissProt (18) Human Mus musculus MOUSE MGI (19) Mouse Rattus norvegicus RAT RGD (20) Rat Saccharomyces cerevisiae YEAST SGD (21) Budding yeast Schizosaccharomyces pombe SCHPO GeneDB (22) Fission yeast Other chordate genomes Ensembl (23) Other non-chordate genomes Entrez Gene (17) Nucleic Acids Research, 2010, Vol....
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...Previously, for genes only identifiers from NCBI Entrez Gene (17) or FlyBase (15) were supported; for proteins only RefSeq (24) or FlyBase identifiers....
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...Previously, for genes only identifiers from NCBI Entrez Gene (17) or Figure 3....
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