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APID specifications

Information


Unique identifier OMICS_02864
Name APID
Alternative name Agile Protein Interaction DataAnalyzer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • APID2NET

Publications for Agile Protein Interaction DataAnalyzer

APID citations

 (43)
library_books

Prediction of cassava protein interactome based on interolog method

2017
Sci Rep
PMCID: 5722940
PMID: 29222529
DOI: 10.1038/s41598-017-17633-2

[…] nformation of these template plants was obtained from Phytozome V9 and Uniprot databases, and the protein interaction information was collected from seven databases; IntAct, MINT, AtPIN, AtPID, PAIR, APID, and PRIN (Fig. ). To find protein orthologs in cassava, we performed BLASTp search against the cassava genome sequence. The cassava orthologous proteins were identified if the identity percentag […]

library_books

Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration and Cancer

2017
Sci Rep
PMCID: 5597608
PMID: 28904337
DOI: 10.1038/s41598-017-10675-6

[…] neurotrophic parasite Toxoplasma gondii. Congenital and postnatal infections with T. gondii persist in all infected persons. The parasite interconverts between slow-growing, encysted bradyzoites and rapid-growing tachyzoites. In mice, T. gondii creates a chronic intra-neuronal infection and an inflammatory process. Mice with acute and chronic infection have alterations in neurotransmitters, memory […]

library_books

Bioinformatics analysis of the proteins interacting with LASP 1 and their association with HBV related hepatocellular carcinoma

2017
Sci Rep
PMCID: 5339786
PMID: 28266596
DOI: 10.1038/srep44017

[…] To investigate the proteins that interact with LASP-1, the information of target human proteins was retrieved from different public databases, including IntAct, BioGRID, APID, PINA2.0, Mentha, HitPredict, WiKi-Pi, PIPs, PPI-finder and PrePPI or from the studies reported in PubMed. A total of 390 predicted or experimentally validated LASP-1 interacting proteins were ob […]

library_books

Path2enet: generation of human pathway derived networks in an expression specific context

2016
BMC Genomics
PMCID: 5088520
PMID: 27801297
DOI: 10.1186/s12864-016-3066-7

[…] lopedia of Genes and Genomes) [, ] and integrates them with gene expression data from various resources as well as experimentally determined data from protein-protein physical interactions taken from APID [, ]. Path2enet tool uses the expression data to determine if a given node (protein) in a generated network is active (ON) or inactive (OFF) in a specific cellular context, cell type or condition […]

library_books

Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks

2016
F1000Res
PMCID: 5105880
PMID: 27853512
DOI: 10.5256/f1000research.9812.r15065

[…] ysis can provide insight into what are the most relevant network features in a particular study or context – .Cytoscape has a number of applications to identify hubs in networks including cytoHubba , APID2Net , PinnacleZ , NetworkAnalyzer , and CentiScaPe , however, only the latter two are compatible with Cytoscape 3+. All of the applications available to date identify hubs based on node connecti […]

library_books

RWCFusion: identifying phenotype specific cancer driver gene fusions based on fusion pair random walk scoring method

2016
Oncotarget
PMCID: 5308635
PMID: 27506935
DOI: 10.18632/oncotarget.11064

[…] types and sources of protein–protein association []. Several other resources that are currently being actively maintained are similar to STRING, such as: VisANT [], GeneMANIA [], N-Browse [], I2D [], APID [] and ConsensusPathDB []. However, STRING is one of the very few sites to hold experimental, predicted and transferred interactions, together with interactions obtained through text mining. What […]

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APID institution(s)
Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CIC, CSIC/USAL), Salamanca, Spain

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