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APID specifications


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



Publications for Agile Protein Interaction DataAnalyzer

APID citations


Prediction of cassava protein interactome based on interolog method

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 […]


Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration and Cancer

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 […]


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

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 […]


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

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 […]


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

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 […]


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

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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