Literature DB >> 16510498

PIANA: protein interactions and network analysis.

Ramon Aragues1, Daniel Jaeggi, Baldo Oliva.   

Abstract

UNLABELLED: We present a software framework and tool called Protein Interactions And Network Analysis (PIANA) that facilitates working with protein interaction networks by (1) integrating data from multiple sources, (2) providing a library that handles graph-related tasks and (3) automating the analysis of protein-protein interaction networks. PIANA can also be used as a stand-alone application to create protein interaction networks and perform tasks such as predicting protein interactions and helping to identify spots in a 2D electrophoresis gel. AVAILABILITY: PIANA is under the GNU GPL. Source code, database and detailed documentation may be freely downloaded from http://sbi.imim.es/piana.

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Year:  2006        PMID: 16510498     DOI: 10.1093/bioinformatics/btl072

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  22 in total

1.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

2.  ModLink+: improving fold recognition by using protein-protein interactions.

Authors:  Oriol Fornes; Ramon Aragues; Jordi Espadaler; Marc A Marti-Renom; Andrej Sali; Baldo Oliva
Journal:  Bioinformatics       Date:  2009-04-08       Impact factor: 6.937

3.  A transcriptome-proteome integrated network identifies endoplasmic reticulum thiol oxidoreductase (ERp57) as a hub that mediates bone metastasis.

Authors:  Naiara Santana-Codina; Rafael Carretero; Rebeca Sanz-Pamplona; Teresa Cabrera; Emre Guney; Baldo Oliva; Philippe Clezardin; Omar E Olarte; Pablo Loza-Alvarez; Andrés Méndez-Lucas; Jose Carlos Perales; Angels Sierra
Journal:  Mol Cell Proteomics       Date:  2013-04-26       Impact factor: 5.911

4.  Expression of endoplasmic reticulum stress proteins is a candidate marker of brain metastasis in both ErbB-2+ and ErbB-2- primary breast tumors.

Authors:  Rebeca Sanz-Pamplona; Ramón Aragüés; Keltouma Driouch; Berta Martín; Baldo Oliva; Miguel Gil; Susana Boluda; Pedro L Fernández; Antonio Martínez; Víctor Moreno; Juan J Acebes; Rosette Lidereau; Fabien Reyal; Marc J Van de Vijver; Angels Sierra
Journal:  Am J Pathol       Date:  2011-06-25       Impact factor: 4.307

5.  Functional pathways shared by liver and lung metastases: a mitochondrial chaperone machine is up-regulated in soft-tissue breast cancer metastasis.

Authors:  Rebeca Sanz; Ramón Aragüés; Verena Stresing; Berta Martín; Thomas Landemaine; Baldo Oliva; Keltouma Driouch; Rosette Lidereau; Angels Sierra
Journal:  Clin Exp Metastasis       Date:  2007-11-16       Impact factor: 5.150

6.  The role of exon shuffling in shaping protein-protein interaction networks.

Authors:  Douglas V Cancherini; Gustavo S França; Sandro J de Souza
Journal:  BMC Genomics       Date:  2010-12-22       Impact factor: 3.969

7.  Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2.

Authors:  Nikolaus Schultz; Dina R Marenstein; Dino A De Angelis; Wei-Qing Wang; Sven Nelander; Anders Jacobsen; Debora S Marks; Joan Massagué; Chris Sander
Journal:  Silence       Date:  2011-03-14

8.  MINT, the molecular interaction database: 2009 update.

Authors:  Arnaud Ceol; Andrew Chatr Aryamontri; Luana Licata; Daniele Peluso; Leonardo Briganti; Livia Perfetto; Luisa Castagnoli; Gianni Cesareni
Journal:  Nucleic Acids Res       Date:  2009-11-06       Impact factor: 16.971

9.  PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440.

Authors:  Seong-Jin Park; Jong-Soon Choi; Byoung-Chul Kim; Seong-Woong Jho; Jea-Woon Ryu; Daeui Park; Kyung-A Lee; Jong Bhak; Seung Il Kim
Journal:  BMC Genomics       Date:  2009-12-03       Impact factor: 3.969

10.  Biana: a software framework for compiling biological interactions and analyzing networks.

Authors:  Javier Garcia-Garcia; Emre Guney; Ramon Aragues; Joan Planas-Iglesias; Baldo Oliva
Journal:  BMC Bioinformatics       Date:  2010-01-27       Impact factor: 3.169

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