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Clustering biological annotations and gene expression data to identify

putatively co-regulated biological processes

Henegar C., Cancello R., et al, JBCB 2006 Aug;4(4):833-52.

Supplementary detailed results to those presented within the paper submitted to JBCB are available below.

Detailed results of FunCluster's discriminatory functional analysis of genes specifically expressed within adipocytes or stroma vascular fraction (SVF) cells (Cancello et al., 2005), based on GO and KEGG annotations as available in March 2004 (supplementary to those presented in our JBCB paper):


Adipocyte Functional Clusters	SVF Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function
KEGG	KEGG

Supplementary results obtained through discriminatory functional analysis of genes specifically expressed within adipocytes or stroma vascular fraction (SVF) cells illustrating FunCluster's behavior for three different thresholds of the Spearman's Rs (see JBCB paper for details) based on GO and KEGG annotations as available in February 2006:
- Rs ≥ 0.85


Adipocyte Functional Clusters	SVF Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function
KEGG	KEGG

Rs ≥ 0.90


Adipocyte Functional Clusters	SVF Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function
KEGG	KEGG

Rs ≥ 0.95


Adipocyte Functional Clusters	SVF Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function
KEGG	KEGG

Supplementary results obtained through discriminatory functional analysis of genes specifically expressed within adipocytes or stroma vascular fraction (SVF) cells illustrating FunCluster's behavior when the automated annotation procedure is restricted to direct GO annotations (see JBCB paper for details) based on GO and KEGG annotations as available in February 2006:


Adipocyte Functional Clusters	SVF Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function

Detailed results of FunCluster's functional analysis of hyperinsulinemic clamp dataset (Rome et al., 2003) , based on GO and KEGG annotations as available in March 2004 (supplementary to those presented in our JBCB paper):


Down-regulated Functional Clusters	Up-regulated Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function
KEGG	KEGG

Supplementary results obtained on the hyperinsulinemic clamp dataset illustrating FunCluster's behavior for three different thresholds of the Spearman's Rs (see JBCB paper for details) based on GO and KEGG annotations as available in February 2006:

Rs ≥ 0.85


Down-regulated Functional Clusters	Up-regulated Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function
KEGG	KEGG

Rs ≥ 0.90


Down-regulated Functional Clusters	Up-regulated Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function
KEGG	KEGG

Rs ≥ 0.95


Down-regulated Functional Clusters	Up-regulated Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function
KEGG	KEGG

Supplementary results obtained on the hyperinsulinemic clamp dataset illustrating FunCluster's behavior when the automated annotation procedure is restricted to direct GO annotations (see JBCB paper for details) based on GO and KEGG annotations as available in February 2006:


Down-regulated Functional Clusters	Up-regulated Functional Clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function

A comparative assessment of the functional profiling approach implemented within FunCluster algorithm with those provided by FatiGO & FatiWise and GOstat functional profiling tools is available below.

Results of a discriminatory functional analysis of genes specifically expressed within adipocytes or stroma vascular fraction (SVF) cells (Cancello et al., 2005) performed with FatiGO & FatiWise and GOstat tools:


FatiGO	FatiWise
GO Biological Process	KEGG
GO Cellular Component
GO Molecular Function



GOstat
Adipocyte GO clusters	SVF GO clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function

Data files used for this analysis can be downloaded here. Three data files are provided including, besides the two lists of genes specifically expressed within adipocytes or SVF cells, a reference list with the ensemble of genes tested for differential expression within the two cellular fractions. These files are specifically formatted as required for their use with the three mentioned tools. Complete expression data needed for FunCluster's functional analysis is provided within the FunCluster R package available from this website or from CRAN repositories.

Results of the functional analysis of genes significantly up or down-regulated within the hyperinsulinemic clamp dataset (Rome et al., 2003) performed with FatiGO & FatiWise and GOstat tools:


FatiGO
Down-regulated Genes	Up-regulated Genes
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function


FatiWise
Down-regulated Genes	Up-regulated Genes
KEGG	KEGG



GOstat
Down-regulated Genes GO clusters	Up-regulated Genes GO clusters
GO Biological Process	GO Biological Process
GO Cellular Component	GO Cellular Component
GO Molecular Function	GO Molecular Function

Data files used for this analysis can be downloaded here. Three data files are provided including, besides the two lists of genes specifically up or down-regulated by insulin, a reference list with the ensemble of genes tested for differential expression. These files are specifically formatted as required for their use with the three mentioned tools. Complete expression data needed for FunCluster's functional analysis is provided within the FunCluster R package available from this website or from CRAN repositories.

Last updated: 04.10.2007