CFDE Gene-Centric Appyter: LINC00987

Given the gene LINC00987, we request information about it from several different DCCs in hopes of creating a comprehensive knowledge report for it.

MyGeneInfo: Query

https://mygene.info/

To interoperate with different APIs which support different gene identifier schemes. We'll first use mygene.info to resolve gene identifiers.

{
    "took": 5,
    "total": 1,
    "max_score": 216.72923,
    "hits": [1 item]
}

GeneID: 100499405

MyGeneInfo

https://mygene.info/

With the Entrez Gene ID, we can resolve lots of different identifiers and identifiability information from mygene.info.

{
    "AllianceGenome": "48911",
    "HGNC": "48911",
    "_id": "100499405",
    "_version": 1,
    "accession": {2 items},
    "ensembl": {4 items},
    "entrezgene": "100499405",
    "exons": [9 items],
    "exons_hg19": [9 items],
    "generif": [2 items],
    "genomic_pos": {5 items},
    "genomic_pos_hg19": {4 items},
    "map_location": "12p13.31",
    "name": "long intergenic non-protein coding RNA 987",
    "refseq": {2 items},
    "reporter": {3 items},
    "symbol": "LINC00987",
    "taxid": 9606,
    "type_of_gene": "ncRNA",
    "umls": {1 item},
    "unigene": "Hs.182314"
}

Gene Symbol: LINC00987


Primary Information

We query DCC APIs to gain insights about the primary information they collect.

GTEx

https://gtexportal.org/home/

We query the GTEx Data through the GTEx API to identify tissue sites that significantly express the gene question.

Gene with identifier LINC00987 currently not available in GTEx
Could not process GTEx output

LINCS

https://lincsproject.org/

L1000 RNAseq Gene Centric Signature Reverse Search (RGCSRS)

An appyter was built for performing Gene Centric signature reverse searches against the LINCS data. Its functionality is repeated here.

BokehJS 2.4.2 successfully loaded.
No information for gene with identifier LINC00987 found in L1000

International Mouse Phenotyping Consortium (IMPC)

https://www.mousephenotype.org/

IMPC contains serves mouse phenotype information associated with gene markers. Its API is described here and allows us to identify phenotypes significantly associated with a gene.

No information for gene with identifier LINC00987 found in IPMC
IPMC Results could not be processed

GlyGen

https://www.glygen.org/

GlyGen collects extensive protein product information related to Glycans and permits accessing that information over their API.

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  warnings.warn(

No information for gene with identifier LINC00987 found in GlyGen

exRNA

https://ldh.clinicalgenome.org/ldh/ui/

The exRNA Linked Data Hub (LDH) facilitates efficient access to collated information such as links and select data from different data sources, which are made available using RESTful APIs. Currently, LDH focuses on linking information about human genes and variants to support exRNA curation efforts.

We provide the gene symbol to exRNA and obtain the reported linked data. The query will produce a document with all associated regulatory element in the +/- 10kb range or overlapping the gene.

Gene with identifier LINC00987 not available in exRNA LDH

HuBMAP

https://hubmapconsortium.org/

The goal of the Human BioMolecular Atlas Program (HuBMAP) is to develop an open and global platform to map healthy cells in the human body.

The HuBMAP ASCT+B Data was processed and is served by Enrichr. This data can be used to associate genes with cell types.

No information for gene with identifier LINC00987 found in HuBMAP ASCT+B

Metabolomics

https://metabolomicsworkbench.org/

The National Institutes of Health (NIH) Common Fund Metabolomics Program was developed with the goal of increasing national capacity in metabolomics by supporting the development of next generation technologies, providing training and mentoring opportunities, increasing the inventory and availability of high quality reference standards, and promoting data sharing and collaboration.

MetGENE identifies the pathways and reactions catalyzed by the given gene LINC00987, its related metabolites and the studies in Metabolomics Workbench with data on such metabolites.

No information for gene with identifier LINC00987 found in MetGene

Secondary Information

Each DCC has assembled a large repository of knowledge besides the data directly collected by the data generation centers they coordinate. We can access this expanded knowledge as well.

IDG

https://druggablegenome.net/

Pharos

We query IDG's knowledge base of targets and their Disease associations through the Pharos API.

No information for gene with identifier LINC00987 found in Pharos
Pharos results could not be processed

Harmonizome

We query the Harmonizome API for associations with various biological entities in a standardized set of numerous omics datasets, as detailed here.

{
    "symbol": "LINC00987",
    "synonyms": [],
    "name": "long intergenic non-protein coding RNA 987",
    "description": "",
    "ncbiEntrezGeneId": 100499405,
    "ncbiEntrezGeneUrl": "http://www.ncbi.nlm.nih.gov/gene/100499405",
    "proteins": [],
    "hgncRootFamilies": [],
    "associations": [802 items]
}
GTEX-O5YT-0007-SM-32PK7/GTEx Tissue Sample Gene Expression ProfilesHCC202/Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV ProfilesGTEX-OHPM-0008-SM-4E3IP/GTEx Tissue Sample Gene Expression ProfilesGTEX-OHPK-0008-SM-4E3JL/GTEx Tissue Sample Gene Expression ProfilesGTEX-NPJ8-0007-SM-2D7VX/GTEx Tissue Sample Gene Expression ProfilesGTEX-XLM4-0008-SM-4AT4W/GTEx Tissue Sample Gene Expression ProfilesGTEX-S95S-0005-SM-2XCEC/GTEx Tissue Sample Gene Expression ProfilesGTEX-X88G-0008-SM-47JWN/GTEx Tissue Sample Gene Expression ProfilesGTEX-XYKS-0008-SM-4BRW6/GTEx Tissue Sample Gene Expression ProfilesT47D/CCLE Cell Line Gene CNV Profiles00.511.522.533.54IALM/CCLE Cell Line Gene CNV ProfilesHEP-2/Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression ProfilesGTEX-UTHO-0011-R2A-SM-3GIKC/GTEx Tissue Sample Gene Expression ProfilesNCIH650/CCLE Cell Line Gene CNV ProfilesGTEX-PVOW-1026-SM-2XCF9/GTEx Tissue Sample Gene Expression ProfilesGTEX-XMD1-0011-R9A-SM-4AT49/GTEx Tissue Sample Gene Expression ProfilesGTEX-U3ZH-0526-SM-3DB75/GTEx Tissue Sample Gene Expression Profileshippocampus (hippocampal formation)_3 yrs_M_12980/Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seqNTERA-2/Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV ProfilesGTEX-X4XX-0011-R2A-SM-3P623/GTEx Tissue Sample Gene Expression Profiles
directionupdownSignificant associations with LINC00987 in IDG's HarmonizomeabsoluteZscorenamenamedirection=downdirection=up

ARCHS4

https://maayanlab.cloud/archs4/

ARCHS4 has processed numerous GEO studies and also has Tissue expression data.

UnitProt

https://www.uniprot.org/

UniProt is a comprehensive database on protein function information. Their Proteins REST API, documented here, can be used for gene-centric queries.

https://www.ebi.ac.uk/proteins/api/genecentric?offset=0&size=100&gene=STAT3