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Improving Human Genome Annotation Using a High-Stringency Proteogenomics Workflow

ABSTRACT: Reanalysis of three large human tissue proteomics datasets using a bespoke GENCODE database and multiOTHER algorithm high confidence pipeline.

INSTRUMENT(S): LTQ Orbitrap Velos, LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Heart, Testis, Adipocyte, Prostate Gland, Lung, Liver, Bladder, Cerebral Cortex, Retina, Lymph Node, Nasopharynx, Natural Killer Cell, Uterine Cervix, Kidney, Blood Platelet, Ovary, Helper T-lymphocyte, Uterus, Mouth, Hair Follicle, Fetus, T-lymphocyte, Colon, Seminal Vesicle, Pancreas, Milk, Spleen, Stomach, Monocyte, Tonsil, Cerebrospinal Fluid, Gall Bladder, Cardia, Thyroid Gland, Esophagus, Female Pudendum, Frontal Lobe, Placenta, Anus, Spinal Cord, Rectum, B-lymphocyte, Breast, Skin, Bone, Ascites, Saliva, Adrenal Gland

SUBMITTER: James Wright

LAB HEAD: Jyoti Choudhary

PROVIDER: PXD002967 | Pride | 2016-05-27

REPOSITORIES: Pride

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Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

Wright James C JC Mudge Jonathan J Weisser Hendrik H Barzine Mitra P MP Gonzalez Jose M JM Brazma Alvis A Choudhary Jyoti S JS Harrow Jennifer J

Nature communications 20160602

Complete annotation of the human genome is indispensable for medical research. The GENCODE consortium strives to provide this, augmenting computational and experimental evidence with manual annotation. The rapidly developing field of proteogenomics provides evidence for the translation of genes into proteins and can be used to discover and refine gene models. However, for both the proteomics and annotation groups, there is a lack of guidelines for integrating this data. Here we report a stringen ...[more]

PMID: 27250503

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