Putative novel functional families in Human ncDNA

The material in this page supplements our recent ISMB 2004 paper:

Gill Bejerano, David Haussler, Mathieu Blanchette. 
"Into the heart of darkness: large-scale clustering of human non-coding DNA.
Bioinformatics (2004 ,Aug 4);20 Suppl 1:I40-I48.

Paper Abstract

MOTIVATION: It is currently believed that the human genome contains about twice as much non-coding functional regions as it does protein-coding genes, yet our understanding of these regions is very limited.
RESULTS: We examine the intersection between syntenically conserved sequences in the human, mouse and rat genomes, and sequence similarities within the human genome itself, in search of families of non-protein-coding elements. For this purpose we develop a graph theoretic clustering algorithm, akin to the highly successful methods used in elucidating protein sequence family relationships. The algorithm is applied to a highly filtered set of about 700,000 human-rodent evolutionarily conserved regions, not resembling any known coding sequence, which encompasses 3.7% of the human genome. From these, we obtain roughly 12,000 non-singleton clusters, dense in significant sequence similarities. Further analysis of genomic location, evidence of transcription and RNA secondary structure reveals many clusters to be significantly homogeneous in one or more characteristics. This subset of the highly conserved non-protein-coding elements in the human genome thus contains rich family-like structures, which merit in-depth analysis.

Human ncDNA Clusters

Two text files are available for download:
Work is in progress to further refine the clustering method and annotate these novel clusters.

Source Code

The source code for the clustering algorithm is currently not available for download.
Please refer to the paper for an exact description of the underlying algorithm.

Gill Bejerano
Last modified: Wed Sep 1 13:56:55 PDT 2004