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Protocols

PINA specifications

Information


Unique identifier OMICS_02960
Name PINA
Alternative name Protein Interaction Network Analysis
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Publications for Protein Interaction Network Analysis

PINA citations

 (43)
library_books

Similarity of the dog and human gut microbiomes in gene content and response to diet

2018
Microbiome
PMCID: 5907387
PMID: 29669589
DOI: 10.1186/s40168-018-0450-3

[…] VA [] for diet effect; see also Additional file : Figure S6 which presents the distance boxplots for all samples, and Additional file : Figure S7, which presents the same results using Unifrac [] and PINA [] distances as an alternative). Specifically, the microbiome of HPLC-fed dogs shows a larger shift than that of LPHC-fed dogs, when compared to the Base diet, which is in line with the similarit […]

library_books

Passing Decisions in Football: Introducing an Empirical Approach to Estimating the Effects of Perceptual Information and Associative Knowledge

2018
Front Psychol
PMCID: 5874613
PMID: 29623057
DOI: 10.3389/fpsyg.2018.00361

[…] tudy, the values for the openness of passing lanes, Euclidean distances, and defensive coverage were linearly transformed to values between 1 and 10. In addition to adjusting model sensitivity (e.g., Pina et al., ), this transformation helps maintain information about the situation-specific distribution of the predictor variables within the variable values. The predictor variables were z-standardi […]

library_books

FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets

2018
BMC Genomics
PMCID: 5836822
PMID: 29504895
DOI: 10.1186/s12864-018-4474-7

[…] [] and IntAct [].There are systems that allow the reconstruction of gene networks for a given set of genes/proteins including FunCoup [], STRING [], Pathway Studio [], Ingenuity Pathway Analysis [], PINA [], GeneMANIA [] and ReactomeFIViz []. These systems use various information sources on interactions of molecular genetic objects, including scientific publications and factual databases. FunCoup […]

library_books

Two missense mutations in KCNQ1 cause pituitary hormone deficiency and maternally inherited gingival fibromatosis

2017
Nat Commun
PMCID: 5668380
PMID: 29097701
DOI: 10.1038/s41467-017-01429-z

[…] m three biological replicates. The high confidence protein–protein interactions data were imported into Cytoscape 3.4.0 for the visualization combined with the known protein-protein interactions from PINA2 (Protein Interaction Network Analysis http://cbg.garvan.unsw.edu.au/pina/). Protein complexes were annotated against CORUM database and Gene Ontology term of biological pathway enrichment analys […]

library_books

From protein protein interactions to protein co expression networks: a new perspective to evaluate large scale proteomic data

2017
EURASIP J Bioinform Syst Biol
PMCID: 5359264
PMID: 28477207
DOI: 10.1186/s13637-017-0059-z

[…] es, like the production of accurate -omics data and the collection of reliable molecular interactions. The most broadly adopted softwares include Cytoscape and its plugins [], VisANT [], atBioNet [], PINA [], and Ingenuity [] which represents a commercial solution. On the contrary, Cytoscape is a software now developed by an international consortium of open-source developers. Figure shows a possi […]

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 obtained […]

Citations

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PINA institution(s)
Cancer Research Program, Sydney, NSW, Australia; Peter Wills Bioinformatics Centre, Garvan Institute of Medical Research, Sydney, NSW, Australia; Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; Genome-Scale Biology Program, Institute of Biomedicine, University of Helsinki, Helsinki, Finland
PINA funding source(s)
Supported by the Cancer Council New South Wales, Australia (grant SRP11-01, ICGC 09-01); National Health and Medical Research Council, Australia (grant 631701); Cancer Institute New South Wales, Australia (grant 10/CRF/ 1-01); Academy of Finland (grant 125826); Avner Nahmani Pancreatic Cancer Foundation; R. T. Hall Trust.

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