A draft map of the human proteome
Citations
9,745 citations
6,201 citations
Cites methods from "A draft map of the human proteome"
...For commercial re-use, please contact journals.permissions@oup.com metabolic pathway resource stored in BioPAX format (16); gene and small-molecule perturbations from the LINCS L1000 data set; NCI-Nature pathways (17); protein complexes from the NURSA project (18); pathways from the PANTHER resource (19); targets of phosphatases from DEPOD (20); human phenotypes from the Human Phenotype Ontology (HPO) (21); genes associated with grants using NIH RePORTER and GeneRIF (22); transcription factor targets computed from the ChIP-seq data from the ENCODE project (23); differentially expressed genes from the Allen Brain Atlas (24); tissue expression extracted from the Genotype-Tissue Expression (GTEx) project (25); protein expression in tissues and cell types from ProteomicsDB (26) and the Human Proteome Map (HPM) (27); genes associated with cell survival from the Achilles Project (28); and more....
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...metabolic pathway resource stored in BioPAX format (16); gene and small-molecule perturbations from the LINCS L1000 data set; NCI-Nature pathways (17); protein complexes from the NURSA project (18); pathways from the PANTHER resource (19); targets of phosphatases from DEPOD (20); human phenotypes from the Human Phenotype Ontology (HPO) (21); genes associated with grants using NIH RePORTER and GeneRIF (22); transcription factor targets computed from the ChIP-seq data from the ENCODE project (23); differentially expressed genes from the Allen Brain Atlas (24); tissue expression extracted from the Genotype-Tissue Expression (GTEx) project (25); protein expression in tissues and cell types from ProteomicsDB (26) and the Human Proteome Map (HPM) (27); genes associated with cell survival from the Achilles Project (28); and more....
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3,375 citations
Cites background from "A draft map of the human proteome"
...Two of the most highly accessed data sets are those coming from the two drafts of the human proteome published in Nature in 2014 (11,12) (PXD000561 and PXD000865, respectively)....
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...In addition to the PX resources, there are other valuable proteomics databases and resources available, providing protein expression information derived from MS proteomics data, most notably the Global Proteome Machine Database (GPMDB) (10), ProteomicsDB (11), the Human Proteome Map (12), MaxQB (13), Chorus, PaxDb (14) and MOPED (Multi-Omics Profiling Expression Database) (15), among others....
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References
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"A draft map of the human proteome" refers background or methods in this paper
...The peptides identified were categorized either as (1) mapping intergenic regions (2) overlapping annotated genes (3) mapping to the intronic regions of existing gene models (4) overlapping annotated genes but translated in alternate reading frame....
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...The databases used were: (1) six-frame-translated human genome database (2) threeframe-translated RefSeq mRNA sequences (3) three-frame-translated pseudogene database with sequences derived from NCBI and Gerstein’s pseudogene database (4) three-frame-translated non-coding RNAs from NONCODE (5) N-terminal peptide database derived from RefSeq mRNA sequences from NCBI and (6) signal peptide database from SignalP and HPRD....
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