Cis-regulatory variations: A study of SNPs around genes showing cis-linkage in segregating mouse populations

doi:10.1186/1471-2164-7-235

BMC Genomics

Volume 7

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Xie T
Anand M
Edwards SW
Li G
Wang SS
Schadt EE

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Research article

Cis-regulatory variations: A study of SNPs around genes showing cis-linkage in segregating mouse populations

Debraj GuhaThakurta¹ , Tao Xie¹ , Manish Anand¹^,4 , Stephen W Edwards¹ , Guoya Li² , Susanna S Wang³ and Eric E Schadt¹

¹Genetics, Rosetta Inpharmatics LLC, a wholly owned subsidiaryof Merck & Co., Inc. 401 Terry Avenue North, Seattle, WA 98109, USA

²Informatics, Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck & Co., Inc. 401 Terry Avenue North, Seattle, WA 98109, USA

³Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1679, USA

⁴Microsoft Corporation, One Microsoft Way, Redmond, WA 98052-6399, USA

author email corresponding author email

BMC Genomics 2006, 7:235doi:10.1186/1471-2164-7-235


Published:	15 September 2006

Additional files

Additional file 1:

All genes showing cis-expression linkage (CEGs) in the two mouse crosses. The mouse cross, the tissue in which the cis-linkage was observed, LocusLink identifier, official gene symbol, physical locations of the genes (UCSC mm4 or NCBI build 32 assembly), and the cis-acting LOD scores are given.

Format: XLS Size: 1.2MB Download file

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Additional file 2:

The complete integrated list of CEGs from BxD and BxH crosses. Gene coordinates are with respect to UCSC mm4 assembly (NCBI build 32). The cis-acting eQTL information of these genes may be obtained from the 1.

Format: XLS Size: 298KB Download file

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Additional file 3:

Comprehensive set of promoter cis-SNPs in CEGs. All cis-SNPs in the promoter (upto 5 Kb upstream gene) of the CEGs, along with their location in conserved mouse-human regions (indicated by 'M-H CONS' in the CONSERVATION column), the predicted transcription factor binding sites perturbed by the SNP, and correlation of the gene to the transcription factors (if p < 0.01) (in cases where there is a transcription factor binding site present that is perturbed by a cis-SNP) are given. All Celera SNPs [20] are now also available through latest release of the public mouse dbSNP database [21]. The public dbSNP identifiers corresponding to the Celera SNPs are therefore provided for reference.

Format: XLS Size: 1MB Download file

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Additional file 4:

Comprehensive set of cis-SNPs in non-coding regions of CEGs. All SNPs in the non-coding region (introns and 5 Kb downstream) of the CEGs, along with their location in conserved mouse-human regions (indicated by 'M-H CONS' in the CONSERVATION column), the predicted transcription factor binding sites perturbed by the SNP, and correlation of the gene to the transcription factors (if p < 0.01) (in cases where there is a transcription factor binding site present that is perturbed by a cis-SNP) are given. dbSNP identifiers corresponding to the Celera SNPs are provided.

Format: XLS Size: 9MB Download file

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Additional file 5:

Gene structure of the CEGs. Exons of all 2,047 CEGs mapped to the UCSC mm4 assembly (NCBI build 32) are given. This data helps in finding where a non-coding cis-SNP is located in the gene.

Format: XLS Size: 1.9MB Download file

This file can be viewed with: Microsoft Excel Viewer