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Protocols

BioCarta specifications

Information


Unique identifier OMICS_23321
Name BioCarta
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

BioCarta citations

 (324)
library_books

Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

2018
Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004

[…] gene expression signature in MAPK-altered samples (p = 0.0018, t test) (A and S6B), further demonstrated by GSEA (e.g., PID_CD8_TCR_ DOWNSTREAM_PATHWAY, enrichment score = 0.551, nominal p = 0.0099; BIOCARTA_TCR_PATHWAY enrichment score = 0.520, nominal p = 0.0305) ().Figure 7We also explored other immune-related gene expression signatures in the RNA-seq data, and noted a trend toward an elevated […]

library_books

VAReporter: variant reporter for cancer research of massive parallel sequencing

2018
BMC Genomics
PMCID: 5954270
PMID: 29764369
DOI: 10.1186/s12864-018-4468-5

[…] Pathway component genes are defined as gene sets collected in the Molecular Signatures Database v5.0 (MSigDB) [] that are curated from KEGG [], BioCarta [], Pathway Interaction Database [], Reactome and Signaling Gateway []. VAReporter can assess the mutational events of pathway component genes and display subsets of patients as pie charts an […]

library_books

Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism

2018
Sci Rep
PMCID: 5940770
PMID: 29739984
DOI: 10.1038/s41598-018-25357-0

[…] nificantly activated in LumA ILC compared to LumA IDC, we queried the induced DE genes in the MSigDB database. Nine of the top 15 induced pathways were immune-related, including Response to Wounding, BioCarta IL17 Pathway, and BioCarta TCR Pathway (Supplementary Fig. , Supplementary Table ). In order to investigate the immune pathway results further, we utilized data from a recent analysis of immu […]

library_books

A side effect free method for identifying cancer drug targets

2018
Sci Rep
PMCID: 5923273
PMID: 29703908
DOI: 10.1038/s41598-018-25042-2

[…] teins by integrating the interactions of protein components of all the pathways related to cancer (Fig. ). These pathways of cancer are the established ones taken from four separate databases namely, BIOCARTA, Pathway Interaction Database (PID), REACTOME and Kyoto Encyclopedia for Genes and Genomes (KEGG) (Fig. ). The interactome is comprised of 129,276 interactions (as per STRING database) arisin […]

library_books

Genome wide pleiotropy and shared biological pathways for resistance to bovine pathogens

2018
PLoS One
PMCID: 5880348
PMID: 29608619
DOI: 10.1371/journal.pone.0194374

[…] CTA software []. Third: a gene-set (Biological pathways) analysis step, to compute biological pathway p-values, using MAGMA (with the “competitive gene-set analysis” function) with publicly available BIOCARTA, KEGG and REACTOME database. All analyses in MAGMA are structured as a linear regression model on gene-level data. Z=β0+β1G1+e(Model – 4) Where Z was the phenotype vector, Gene-sets G1 were b […]

call_split

Concurrent Host Pathogen Transcriptional Responses in a Clostridium perfringens Murine Myonecrosis Infection

2018
MBio
PMCID: 5874911
PMID: 29588405
DOI: 10.1128/mBio.00473-18
call_split See protocol

[…] road categories by which to describe the nature of the host response. These often have different emphases such as broad biological processes (KEGG), protein interactions (PID), or molecular pathways (biocarta) or combinations (Hallmark). Functional characterization categories for upregulated bacterial and host genes were also identified using the bioconductor “GOseq” package () and analysis tools […]

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