Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features

doi:10.1186/1471-2105-7-147

BMC Bioinformatics

Volume 7

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Methodology article

Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features

JR Semeiks¹ , A Rizki¹ , MJ Bissell¹ and IS Mian²

¹Life Sciences Division (MS 977-225A), Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA

²Life Sciences Division (MS 74-197), Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720-8265, USA

author email corresponding author email

BMC Bioinformatics 2006, 7:147doi:10.1186/1471-2105-7-147


Published:	16 March 2006

Additional files

Additional File 1:

Information on the 52 genes in the LUMINAL collection. For each gene, the "LocusID", "Symbol", "Name", "Cytoband Location", "GO Terms", "Domain Terms", "KEGG Pathway" and "OMIM" fields contain data taken from the July 2004 release of LocusLink. Genes are grouped by their assigned consensus clusters and ordered by their cytoband locations within each cluster. The GO and CDD terms shown are attributes in the gene attribute profiles used as input for probablistic clustering (explicit terms assigned to a gene by LocusLink plus implicit GO terms). The attributes marked with an asterisk are influential attributes, GO/CDD terms that occur with a frequency > 0.5 in clusters with two or more genes.

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Additional File 2:

Information on the GO and CDD attributes associated with the consensus clusters discovered for genes in the LUMINAL collection. For each consensus cluster, the file shows the number of genes assigned to the cluster, along with the absolute count and relative frequency of all attributes associated with the cluster's genes. The section labeled "Summary" shows all the attributes associated with genes in the data set, ordered by average count across all consensus clusters.

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Additional File 3:

Information on the 89 genes in the consensus clusters discovered and characterized for the MYOEPITHELIAL collection, along with their associated GO and CDD attributes. The formats are the same as for luminal-all.html and luminal-attrfreq.html.

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Additional File 4:

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Additional File 5:

Information on the chromosomal locations of the luminal epithelial (brown) and myoepithelial (green) genes. For each gene, the "LocusID" and "Symbol" fields are taken from the July 2004 release of LocusLink. The "Cytoband", "Start" and "End" fields are taken from the May 2004 UCSC assembly of the human genome. Genes are ordered by chromosomal coordinates (p arm followed by q arm). The "Overall" column indicates the distance in kilobases between the adjacent transcription end and start coordinates of the two closest genes from the union of the LUMINAL and MYOEPITHELIAL collections, as well as the number of RefSeqs found in this interval. "pter" and "qter" indicate the number of genes from a telomere to the closest gene in either collection.

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