Analyzing and interpreting genome data at the network level with ConsensusPathDB

By Ralf Herwig, C. Hardt, M. Lienhard, Atanas Kamburov. Nature Protocols, 2016

396 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/22e66a75b38da6cba51edb58aba173aebabd32ff

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

FMRP Modulates Neural Differentiation through m6A-Dependent mRNA Nuclear Export (2019, positive): “Pathway analysis was performed using Consensus PathDB (Herwig et al., 2016).”
Derivation of Human Trophoblast Stem Cells. (2018, positive): “We then conducted functional annotation of the gene lists using ConsensusPathDB (Herwig et al., 2016; Figure 1A).”
The BioGRID interaction database: 2019 update (2018, background): “Comparatively few data resources combine chemical– protein interaction data with relevant protein interactions but include STITCH (56), ConsensusPathDB (57), SuperTarget (58) and IntAct (59).”
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets (2018, background): “The STRING database (‘Search Tool for Retrieval of Interacting Genes / Proteins’) belongs to this latter class, along with GeneMania (22), FunCoup (23), I2D (24), ConsensusPathDb (25), IMP (26) and HumanNet (27)––most of which have recently been reviewed and benchmarked in (7).”
Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation (2017, positive): “Analysis of enrichment for Wikipathways terms was performed using ConsensusPathDB (Herwig et al., 2016), which calculates enrichment p values using the Wilcoxon’s matched-pairs signed-rank test, and Benjamini Hochberg FDR correction.”
Cooperation between Constitutive and Inducible Chemokines Enables T-cell Engraftment and Immune Attack in Solid Tumors (2019, background): “A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript heatmap for gene sets in BioCarta and Wikipathways in the top 202 differentially expressed genes characteristic for the Hi-Hi groups in five”