CFDE Gene-Centric Appyter: LAMB2

Given the gene LAMB2, 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": 8,
    "total": 656,
    "max_score": 142.41003,
    "hits": [10 items]
}

GeneID: 3913

MyGeneInfo

https://mygene.info/

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

{
    "AllianceGenome": "6487",
    "HGNC": "6487",
    "MIM": "150325",
    "_id": "3913",
    "_version": 1,
    "accession": {4 items},
    "alias": [3 items],
    "ensembl": {5 items},
    "entrezgene": "3913",
    "exac": {9 items},
    "exons": [1 item],
    "exons_hg19": [1 item],
    "generif": [32 items],
    "genomic_pos": {5 items},
    "genomic_pos_hg19": {4 items},
    "go": {3 items},
    "homologene": {2 items},
    "interpro": [4 items],
    "ipi": [2 items],
    "map_location": "3p21.31",
    "name": "laminin subunit beta 2",
    "other_names": [6 items],
    "pantherdb": {4 items},
    "pathway": {6 items},
    "pfam": [3 items],
    "pharmgkb": "PA164741827",
    "pharos": {2 items},
    "pir": [2 items],
    "prosite": [3 items],
    "reagent": {6 items},
    "refseq": {4 items},
    "reporter": {6 items},
    "summary": "Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins, composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively), form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. Several isoforms of each chain have been described. Different alpha, beta and gamma chain isomers combine to give rise to different heterotrimeric laminin isoforms which are designated by Arabic numerals in the order of their discovery, i.e. alpha1beta1gamma1 heterotrimer is laminin 1. The biological functions of the different chains and trimer molecules are largely unknown, but some of the chains have been shown to differ with respect to their tissue distribution, presumably reflecting diverse functions in vivo. This gene encodes the beta chain isoform laminin, beta 2. The beta 2 chain contains the 7 structural domains typical of beta chains of laminin, including the short alpha region. However, unlike beta 1 chain, beta 2 has a more restricted tissue distribution. It is enriched in the basement membrane of muscles at the neuromuscular junctions, kidney glomerulus and vascular smooth muscle. Transgenic mice in which the beta 2 chain gene was inactivated by homologous recombination, showed defects in the maturation of neuromuscular junctions and impairment of glomerular filtration. Alternative splicing involving a non consensus 5' splice site (gc) in the 5' UTR of this gene has been reported. It was suggested that inefficient splicing of this first intron, which does not change the protein sequence, results in a greater abundance of the unspliced form of the transcript than the spliced form. The full-length nature of the spliced transcript is not known. [provided by RefSeq, Aug 2011].",
    "symbol": "LAMB2",
    "taxid": 9606,
    "type_of_gene": "protein-coding",
    "umls": {1 item},
    "unigene": "Hs.439726",
    "uniprot": {2 items},
    "wikipedia": {1 item}
}

Gene Symbol: LAMB2


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 LAMB2 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.
Top CRISPR KO signatures where LAMB2 is up-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
XPR028_HT29.311_96H_A24_OAZ1 0.0333 1.1925 0.253934 1756.0 OAZ1 HT29.311 96h
XPR036_PC3.311B_96H_O07_MVK 0.0294 1.1571 0.210459 1922.0 MVK PC3.311B 96h
XPR022_HT29.311_96H_A07_PRPF38B 0.0325 1.1411 0.190397 1192.0 PRPF38B HT29.311 96h
XPR028_HT29.311_96H_O16_NDUFS2 0.0318 1.1352 0.182926 2452.0 NDUFS2 HT29.311 96h
XPR031_HT29.311_96H_A06_PDCD1LG2 0.0322 1.1125 0.153847 2248.0 PDCD1LG2 HT29.311 96h
XPR032_A549.311_96H_C16_FFAR2 0.0286 1.1095 0.149919 1052.0 FFAR2 A549.311 96h
XPR033_MCF7.311_96H_L22_P2RY4 0.0280 1.1023 0.140539 1948.0 P2RY4 MCF7.311 96h
XPR018_MCF7.311_96H_F22_JUN 0.0298 1.0944 0.130194 2399.0 JUN MCF7.311 96h
XPR024_BICR6.311_96H_H24_CCNA2 0.0302 1.0884 0.122256 2032.0 CCNA2 BICR6.311 96h
XPR015_MCF7.311_96H_O20_CRHBP 0.0294 1.0801 0.111119 2570.0 CRHBP MCF7.311 96h
Top CRISPR KO signatures where LAMB2 is down-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
XPR028_HT29.311_96H_I05_SLC25A12 -0.0407 0.8381 -0.254835 1293.0 SLC25A12 HT29.311 96h
XPR030_HT29.311_96H_I12_PSMB1 -0.0294 0.8473 -0.239023 2628.0 PSMB1 HT29.311 96h
XPR011_MCF7.311_96H_N03_AFF3 -0.0299 0.8585 -0.220097 1811.0 AFF3 MCF7.311 96h
XPR019_HT29.311_96H_M17_KIF21B -0.0318 0.8671 -0.205702 1284.0 KIF21B HT29.311 96h
XPR028_HT29.311_96H_F16_TRPV2 -0.0314 0.8718 -0.197866 1371.0 TRPV2 HT29.311 96h
XPR012_PC3.311B_96H_N03_BST2 -0.0281 0.8778 -0.188097 2110.0 BST2 PC3.311B 96h
XPR034_U251MG.311_96H_F03_PLK4 -0.0282 0.8872 -0.172600 1906.0 PLK4 U251MG.311 96h
XPR028_HT29.311_96H_E05_COX5B -0.0299 0.8958 -0.158824 1528.0 COX5B HT29.311 96h
XPR023_MCF7.311_96H_E18_RSAD2 -0.0299 0.8959 -0.158537 2637.0 RSAD2 MCF7.311 96h
XPR012_HT29.311_96H_M23_ARRDC5 -0.0317 0.8997 -0.152490 2115.0 ARRDC5 HT29.311 96h
Top Chemical Perturbation signatures where LAMB2 is up-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
AICHI002_NALM6_24H_H07_MLN-4924_10uM -0.0321 1.4377 0.523753 2676.0 MLN-4924 10uM NALM6 24h
REP.B027_JURKAT_24H_K20_thiothixene_0.74uM 0.0323 1.3011 0.379727 467.0 thiothixene 0.74uM JURKAT 24h
REP.B008_THP1_24H_C12_glibenclamide_0.01uM 0.0341 1.2275 0.295778 1123.0 glibenclamide 0.01uM THP1 24h
ASG002_NCIH2110_24H_F11_floxuridine_1.11uM 0.0365 1.2154 0.281427 1993.0 floxuridine 1.11uM NCIH2110 24h
REP.A024_THP1_24H_J20_NVP-DPP728_3.33uM 0.0334 1.2005 0.263664 1449.0 NVP-DPP728 3.33uM THP1 24h
MOAR012_CJM_24H_P05_calmidazolium_3.33uM 0.0311 1.1716 0.228419 1844.0 calmidazolium 3.33uM CJM 24h
REP.B027_THP1_24H_O20_timonacic_0.74uM 0.0345 1.1569 0.210247 586.0 timonacic 0.74uM THP1 24h
REP.A010_THP1_24H_G20_methazolamide_3.33uM 0.0325 1.1563 0.209512 512.0 methazolamide 3.33uM THP1 24h
REP.A014_A549_24H_J02_PHA-848125_3.33uM 0.0309 1.1409 0.190227 2985.0 PHA-848125 3.33uM A549 24h
MOAR008_BEN_24H_O23_etoricoxib_3.33uM 0.0379 1.1343 0.181817 1687.0 etoricoxib 3.33uM BEN 24h
Top Chemical Perturbation signatures where LAMB2 is down-regulated (based on fold change)
CD Coefficient Fold Change Log2(Fold Change) Rank in Signature Perturbagen Dose Cell Line Timepoint
Signature
AICHI002_OCILY3_24H_C02_CP-466722_2.5uM -0.0323 0.6511 -0.619053 843.0 CP-466722 2.5uM OCILY3 24h
REP.A025_JURKAT_24H_L17_topiroxostat_0.125uM -0.0385 0.6590 -0.601628 573.0 topiroxostat 0.125uM JURKAT 24h
AICHI001_OCILY10_24H_H03_ruxolitinib_0.66uM 0.0321 0.6905 -0.534290 1072.0 ruxolitinib 0.66uM OCILY10 24h
REP.A024_THP1_24H_K23_oxiperomide_0.125uM -0.0383 0.7574 -0.400840 731.0 oxiperomide 0.125uM THP1 24h
REP.A015_THP1_24H_C18_amonafide_0.04uM -0.0318 0.7910 -0.338182 1284.0 amonafide 0.04uM THP1 24h
REP.A024_THP1_24H_M05_regadenoson_0.125uM -0.0318 0.7927 -0.335124 852.0 regadenoson 0.125uM THP1 24h
PBIOA015_PC3_24H_J08_tretinoin_3.33uM -0.0376 0.8055 -0.311997 1429.0 tretinoin 3.33uM PC3 24h
LJP005_MCF7_24H_I12_CP-466722_0.04uM -0.0379 0.8360 -0.258409 3626.0 CP-466722 0.04uM MCF7 24h
LJP005_MCF7_24H_C15_vemurafenib_1.11uM -0.0337 0.8419 -0.248282 2884.0 vemurafenib 1.11uM MCF7 24h
ASG002_LNCAP.FGC_24H_O16_parbendazole_10uM -0.0325 0.8540 -0.227719 1622.0 parbendazole 10uM LNCAP.FGC 24h

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 LAMB2 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.

/usr/local/lib/python3.8/dist-packages/urllib3/connectionpool.py:1043: InsecureRequestWarning: Unverified HTTPS request is being made to host 'api.glygen.org'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/1.26.x/advanced-usage.html#ssl-warnings

  warnings.warn(

No information for gene with identifier LAMB2 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.

{
    "data": {11 items},
    "metadata": {1 item},
    "status": {2 items}
}

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.

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 LAMB2, its related metabolites and the studies in Metabolomics Workbench with data on such metabolites.


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.

Abnormality of the corneaCognition DisordersMedulloblastomaMyasthenic Syndromes, CongenitalNEPHROTIC SYNDROME, TYPE 5, WITH OR WITHOUT OCULAR ABNORMALITIESNephrotic syndrome 5 with or without ocular abnormalitiesNephrotic syndrome, type 5, with or without ocular abnormalitiesPierson syndromeProstate cancercongenital myasthenic syndromemedulloblastomapancreatic ductal carcinomaprostate cancerpancreatic ductal adenocarcinoma liver metastasissubependymal giant cell astrocytoma0246810
Disease known to be associated with LAMB2 from IDG's Pharos-logp(combined_stouffer_statistic)name

Harmonizome

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

{
    "symbol": "LAMB2",
    "synonyms": [2 items],
    "name": "laminin, beta 2 (laminin S)",
    "description": "Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins, composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively), form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. Several isoforms of each chain have been described. Different alpha, beta and gamma chain isomers combine to give rise to different heterotrimeric laminin isoforms which are designated by Arabic numerals in the order of their discovery, i.e. alpha1beta1gamma1 heterotrimer is laminin 1. The biological functions of the different chains and trimer molecules are largely unknown, but some of the chains have been shown to differ with respect to their tissue distribution, presumably reflecting diverse functions in vivo. This gene encodes the beta chain isoform laminin, beta 2. The beta 2 chain contains the 7 structural domains typical of beta chains of laminin, including the short alpha region. However, unlike beta 1 chain, beta 2 has a more restricted tissue distribution. It is enriched in the basement membrane of muscles at the neuromuscular junctions, kidney glomerulus and vascular smooth muscle. Transgenic mice in which the beta 2 chain gene was inactivated by homologous recombination, showed defects in the maturation of neuromuscular junctions and impairment of glomerular filtration. Alternative splicing involving a non consensus 5' splice site (gc) in the 5' UTR of this gene has been reported. It was suggested that inefficient splicing of this first intron, which does not change the protein sequence, results in a greater abundance of the unspliced form of the transcript than the spliced form. The full-length nature of the spliced transcript is not known. [provided by RefSeq, Aug 2011]",
    "ncbiEntrezGeneId": 3913,
    "ncbiEntrezGeneUrl": "http://www.ncbi.nlm.nih.gov/gene/3913",
    "proteins": [1 item],
    "hgncRootFamilies": [1 item],
    "associations": [5864 items]
}
BRD-K55237592/LINCS L1000 CMAP Chemical Perturbation Consensus SignaturesBRD-K50746465/LINCS L1000 CMAP Chemical Perturbation Consensus SignaturesBRD-K87593103/LINCS L1000 CMAP Chemical Perturbation Consensus SignaturesBRD-K30025024/LINCS L1000 CMAP Chemical Perturbation Consensus SignaturesBRD-K63394284/LINCS L1000 CMAP Chemical Perturbation Consensus SignaturesBRD-K87412446/LINCS L1000 CMAP Chemical Perturbation Consensus SignaturesBRD-K71607378/LINCS L1000 CMAP Chemical Perturbation Consensus SignaturesBRD-K52859120/LINCS L1000 CMAP Chemical Perturbation Consensus Signatureskasugamycin/LINCS L1000 CMAP Chemical Perturbation Consensus SignaturesPCI-15A/COSMIC Cell Line Gene CNV Profiles0246810KP1N/DepMap CRISPR Gene DependencyGTEx SmallIntestine 20-29 vs 50-59/GTEx Tissue-Specific Aging SignaturesJHUEM1/DepMap CRISPR Gene DependencyLOXIMVI_SKIN/CCLE Cell Line Proteomicst58-heart_consensus/MoTrPAC Rat Endurance Exercise TrainingOVCA420/DepMap CRISPR Gene DependencyOCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE/CCLE Cell Line ProteomicsGIMEN/DepMap CRISPR Gene DependencyREH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE/CCLE Cell Line ProteomicsSKMG1/DepMap CRISPR Gene Dependency
directionupdownSignificant associations with LAMB2 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