Bioinformatics approaches for the functional interpretation of protein lists: From ontology term enrichment to network analysis

GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms

(2014) Jia-Hong Wang et al.   BIOINFORMATICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

KinomeXplorer: an integrated platform for kinome biology studies

(2014) Heiko Horn et al.   NATURE METHODS

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

(2014) Roser Corominas et al.   Nature Communications

Human cognitive ability is influenced by genetic variation in components of postsynaptic signalling complexes assembled by NMDA receptors and MAGUK proteins

(2014) W D Hill et al.   Translational Psychiatry

Topologically inferring risk-active pathways toward precise cancer classification by directed random walk

(2013) Wei Liu et al.   BIOINFORMATICS

Gene-set analysis is severely biased when applied to genome-wide methylation data

(2013) Paul Geeleher et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies

(2013) Wilson Wen Bin Goh et al.   BMC GENOMICS

Gene set analysis methods: statistical models and methodological differences

(2013) H. Maciejewski   BRIEFINGS IN BIOINFORMATICS

Networks in proteomics analysis of cancer

(2013) Wilson Wen Bin Goh et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational proteomics: designing a comprehensive analytical strategy

(2013) Wilson Wen Bin Goh et al.   DRUG DISCOVERY TODAY

The Coming of Age of Phosphoproteomics—from Large Data Sets to Inference of Protein Functions

(2013) Philippe P. Roux et al.   MOLECULAR & CELLULAR PROTEOMICS

Evolution and functional cross-talk of protein post-translational modifications

(2013) Pedro Beltrao et al.   Molecular Systems Biology

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

STITCH 4: integration of protein–chemical interactions with user data

(2013) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

CoCiter: An Efficient Tool to Infer Gene Function by Assessing the Significance of Literature Co-Citation

(2013) Nan Qiao et al.   PLoS One

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

(2013) Adi L. Tarca et al.   PLoS One

The challenge of the proteome dynamic range and its implications for in-depth proteomics

(2013) Roman A. Zubarev   PROTEOMICS

Machine learning applications in proteomics research: How the past can boost the future

(2013) Pieter Kelchtermans et al.   PROTEOMICS

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

(2013) Alexandra M. Schnoes et al.   PLoS Computational Biology

Methods and approaches in the topology-based analysis of biological pathways

(2013) Cristina Mitrea et al.   Frontiers in Physiology

Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures

(2013) Amir B.K. Foroushani et al.   PeerJ

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

(2012) Marcus Bantscheff et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

More power via graph-structured tests for differential expression of gene networks

(2012) Laurent Jacob et al.   Annals of Applied Statistics

A quick guide to biomolecular network studies: Construction, analysis, applications, and resources

(2012) Hailin Tang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

EnrichNet: network-based gene set enrichment analysis

(2012) Enrico Glaab et al.   BIOINFORMATICS

THINK Back: KNowledge-based Interpretation of High Throughput data

(2012) Fernando Farfán et al.   BMC BIOINFORMATICS

Fold change and p-value cutoffs significantly alter microarray interpretations

(2012) Mark R Dalman et al.   BMC BIOINFORMATICS

Pathway Distiller - multisource biological pathway consolidation

(2012) Mark S Doderer et al.   BMC GENOMICS

A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics

(2012) Ellen Van Damme et al.   International Journal of Biological Sciences

Integrated Proteomic, Transcriptomic, and Biological Network Analysis of Breast Carcinoma Reveals Molecular Features of Tumorigenesis and Clinical Relapse

(2012) Marcin Imielinski et al.   MOLECULAR & CELLULAR PROTEOMICS

Deciphering a global network of functionally associated post-translational modifications

(2012) Pablo Minguez et al.   Molecular Systems Biology

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

(2012) Pablo Minguez et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores

(2012) Martin H. Schaefer et al.   PLoS One

How advancement in biological network analysis methods empowers proteomics

(2012) Wilson W. B. Goh et al.   PROTEOMICS

Mass spectrometry-based proteomics strategies for protease cleavage site identification

(2012) Bart H. J. van den Berg et al.   PROTEOMICS

A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments

(2012) Melissa M. Matzke et al.   PROTEOMICS

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems

(2011) L. Geistlinger et al.   BIOINFORMATICS

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

(2011) Adriano Barbosa-Silva et al.   BMC BIOINFORMATICS

The representation of protein complexes in the Protein Ontology (PRO)

(2011) Carol J Bult et al.   BMC BIOINFORMATICS

Proteomic patterns of cervical cancer cell lines, a network perspective

(2011) Juan Higareda-Almaraz et al.   BMC Systems Biology

Gene set enrichment analysis: performance evaluation and usage guidelines

(2011) J.-H. Hung et al.   BRIEFINGS IN BIOINFORMATICS

Network-Based Pipeline for Analyzing MS Data: An Application toward Liver Cancer

(2011) Wilson Wen Bin Goh et al.   JOURNAL OF PROTEOME RESEARCH

Protein identification using MS/MS data

(2011) John S. Cottrell   Journal of Proteomics

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications

(2011) Noor Remmerie et al.   PHYTOCHEMISTRY

Less label, more free: Approaches in label-free quantitative mass spectrometry

(2011) Karlie A. Neilson et al.   PROTEOMICS

Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information

(2011) M. C. Good et al.   SCIENCE

Genome-wide transcription factor binding: beyond direct target regulation

(2011) Kyle L. MacQuarrie et al.   TRENDS IN GENETICS

INOH: ontology-based highly structured database of signal transduction pathways

(2011) S. Yamamoto et al.   Database-The Journal of Biological Databases and Curation

De-correlating expression in gene-set analysis

(2010) D. Nam   BIOINFORMATICS

The necessity of adjusting tests of protein category enrichment in discovery proteomics

(2010) Brenton Louie et al.   BIOINFORMATICS

GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach

(2010) Song Zhang et al.   BIOINFORMATICS

Lists2Networks: Integrated analysis of gene/protein lists

(2010) Alexander Lachmann et al.   BMC BIOINFORMATICS

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships

(2010) Adriano Barbosa-Silva et al.   BMC BIOINFORMATICS

Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)

(2010) Elina Tjioe et al.   BMC BIOINFORMATICS

Consistency, comprehensiveness, and compatibility of pathway databases

(2010) Donny Soh et al.   BMC BIOINFORMATICS

A Novel microRNA and transcription factor mediated regulatory network in schizophrenia

(2010) An-Yuan Guo et al.   BMC Systems Biology

Literature-aided interpretation of gene expression data with the weighted global test

(2010) R. Jelier et al.   BRIEFINGS IN BIOINFORMATICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Application of Chemoproteomics to Drug Discovery: Identification of a Clinical Candidate Targeting Hsp90

(2010) Patrick Fadden et al.   CHEMISTRY & BIOLOGY

Large-scale protein interactome mapping: strategies and opportunities

(2010) Sam Lievens et al.   Expert Review of Proteomics

In SituProteomic Analysis of Human Breast Cancer Epithelial Cells Using Laser Capture Microdissection: Annotation by Protein Set Enrichment Analysis and Gene Ontology

(2010) Sangwon Cha et al.   MOLECULAR & CELLULAR PROTEOMICS

Candidate Serological Biomarkers for Cancer Identified from the Secretomes of 23 Cancer Cell Lines and the Human Protein Atlas

(2010) Chih-Ching Wu et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

(2010) Jelle Van Leene et al.   Molecular Systems Biology

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

MicroRNA control of signal transduction

(2010) Masafumi Inui et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Post-translational modifications in signal integration

(2010) Yonathan Lissanu Deribe et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

PHOSIDA 2011: the posttranslational modification database

(2010) F. Gnad et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

From proteome lists to biological impact- tools and strategies for the analysis of large MS data sets

(2010) Rainer Malik et al.   PROTEOMICS

Discussion on common data analysis strategies used in MS-based proteomics

(2010) Rune Matthiesen et al.   PROTEOMICS

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

(2010) Javier De Las Rivas et al.   PLoS Computational Biology

Identification of functional modules that correlate with phenotypic difference: the influence of network topology

(2010) Jui-Hung Hung et al.   GENOME BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

Bioinformatics analysis of mass spectrometry-based proteomics data sets

(2009) Chanchal Kumar et al.   FEBS LETTERS

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

Analysis of Gene Sets Based on the Underlying Regulatory Network

(2009) Ali Shojaie et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Network-assisted protein identification and data interpretation in shotgun proteomics

(2009) Jing Li et al.   Molecular Systems Biology

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Martini: using literature keywords to compare gene sets

(2009) Theodoros G. Soldatos et al.   NUCLEIC ACIDS RESEARCH

Novel Protein-Protein Interactions Inferred from Literature Context

(2009) Herman H. H. B. M. van Haagen et al.   PLoS One

A post-translational modification code for transcription factors: sorting through a sea of signals

(2009) Bérénice A. Benayoun et al.   TRENDS IN CELL BIOLOGY

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization

(2008) Wen-Lin Huang et al.   BMC BIOINFORMATICS

Gene-set approach for expression pattern analysis

(2008) D. Nam et al.   BRIEFINGS IN BIOINFORMATICS

Gene-set analysis and reduction

(2008) I. Dinu et al.   BRIEFINGS IN BIOINFORMATICS

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

Bioinformatics applications for pathway analysis of microarray data

(2008) Thomas Werner   CURRENT OPINION IN BIOTECHNOLOGY

CoPub: a literature-based keyword enrichment tool for microarray data analysis

(2008) R. Frijters et al.   NUCLEIC ACIDS RESEARCH

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis

(2008) Qi Zheng et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY

A survey of visualization tools for biological network analysis

(2008) Georgios A Pavlopoulos et al.   BioData Mining

Anni 2.0: a multipurpose text-mining tool for the life sciences

(2008) Rob Jelier et al.   GENOME BIOLOGY