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|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
Biobase, annotate, GO.db, cluster, Runit
No version available
- person_outline Kristian Ovaska
Publications for csbl.go
Deregulated expression of HDAC9 in B cells promotes development of lymphoproliferative disease and lymphoma in mice
[…] ch Tool for the Retrieval of Interacting Genes/Proteins STRING v9.1 (http://string-db.org) to develop interactomes or networks () and the KEGG pathway database (). GO () clustering was performed with csbl.go (). Partek Genomics Suite 6.6 was additionally used for data set analysis and comparisons. […]
TopoICSim: a new semantic similarity measure based on gene ontology
[…] The R programming language (version 3.2.2) was used for developing and running all programs. We used all the EC codes as annotation terms. The ppiPre (version 1.9), GeneSemSim (version 1.28.2), and csbl.go (version 1.4.1) packages were used to calculate IntelliGO, Wang, and SimGIC measures [–]. The DC values were estimated using the energy (version 1.6.2) package . The SOM algorithm was perfor […]
Insights from systems pharmacology into cardiovascular drug discovery and therapy
[…] n (MF) branches of the Gene Ontology (GO) from the GO database . GO-based semantic similarity scores (GSS) between cardiovascular targets and genes were calculated according to Resnik , using the csbl.go R package  selecting the option to use all three ontologies. We calculated the average GSS of all pairs of cardiovascular target and gene. Random controls were obtained by selecting the same […]
Functional Network Based Gene Set Analysis Using Gene Ontology
[…] ations when calculating the pair-wise gene-gene similarities.To construct the functional network for the various GOGANPA variants, we first obtain pairwise gene similarity matrix using the R package csbl.go , version 1.3.6, available from the package website. We only use GO Biological Process functional annotations for similarity calculation. To obtain the adjacency matrix , the power-law goodnes […]
The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?
[…] ulated in all three GO subsystems: "biological process", "molecular function", "cellular component", employing an R package for computing semantic similarity based on Gene Ontology annotations called csbl.go . […]
Functional organization and its implication in evolution of the human protein protein interaction network
[…] ce was used because it considers the dependence of the annotation terms, which is reflected in the covariance matrix. We also used a two-step semantic similarity based method implemented by R package csbl.go . In this method, the semantic similarity between each pair of GO annotation terms was first computed according to Resnik  and gene functional similarity was then measured by the maximum o […]
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