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Open Access Research article

Functional annotation of novel lineage-specific genes using co-expression and promoter analysis

Charu G Kumar1, Robin E Everts13, Juan J Loor1 and Harris A Lewin12*

Author Affiliations

1 Department of Animal Sciences, University of Illinois at Urbana-Champaign, 210 Edward R Madigan Laboratory, 1201 W Gregory Dr, Urbana, IL 61801, USA

2 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Room 1608, Urbana, IL 61801, USA

3 Current address: SEQUENOM, Inc, 3595 John Hopkins Court, San Diego, CA 92121, USA

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BMC Genomics 2010, 11:161  doi:10.1186/1471-2164-11-161

Published: 9 March 2010

Additional files

Additional file 1:

Tissue expression profile of the LIVR cluster of genes. Tissue expression profile of the LIVR cluster of genes includes two of the LSTs (237NG, 5BP) and 104/208 other genes in the cluster. L_Intestine, large intestine; M_L_Node, mesenteric lymph node; S_Intestine, small intestine.

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Open Data

Additional file 2:

Comparison of ANN-Spec. ab initio predicted motif PWMs with known Transfac binding site PWMs. This table displays the frequency logos of PWMs that were predicted using ANN-Spec and for known Transfac binding sites with which the predicted PWMs were significantly matched.

Format: PDF Size: 498KB Download file

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Open Data

Additional file 3:

Multiple alignment of 34FL with mouse SSLP-1. Multiple alignment of 34FL with mouse SSLP-1 and other secreted Ly6 domain containing proteins having 10 conserved cysteine residues. Dashes in the alignment indicate gaps, and gray shaded areas indicate conserved cysteines.

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Open Data

Additional file 4:

Functions of gene products. Text file containing glossary of gene functions.

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Open Data

Additional file 5:

LSTs used for clustering with tissue expression data. Initial set of 49 LSTs used as seeds to cluster the tissue expression data.

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Open Data