Biomedical subjects

Wes Barris

Publications and source records attributed to Wes Barris.

4 recordsLinked to original sources

PubMed2006

A gene coexpression network for bovine skeletal muscle inferred from microarray data.

We present the application of large-scale multivariate mixed-model equations to the joint analysis of nine gene expression experiments in beef cattle muscle and fat tissues with a total of 147 hybridizations, and we explore 47 experimental conditions or treatments. Using a correlation-based method, we constructed a gene network for 822 genes. Modules of muscle structural proteins and enzymes, extracellular matrix, fat metabolism, and protein synthesis were clearly evident. Detailed analysis of the network identified groupings of proteins on the basis of physical association. For example, expression of three components of the z-disk, MYOZ1, TCAP, and PDLIM3, was significantly correlated. In contrast, expression of these z-disk proteins was not highly correlated with the expression of a cluster of thick (myosins) and thin (actin and tropomyosins) filament proteins or of titin, the third major filament system. However, expression of titin was itself not significantly correlated with the cluster of thick and thin filament proteins and enzymes. Correlation in expression of many fast-twitch muscle structural proteins and enzymes was observed, but slow-twitch-specific proteins were not correlated with the fast-twitch proteins or with each other. In addition, a number of significant associations between genes and transcription factors were also identified. Our results not only recapitulate the known biology of muscle but have also started to reveal some of the underlying associations between and within the structural components of skeletal muscle.

Adipose Tissue↗

PubMed2006

A first-generation metric linkage disequilibrium map of bovine chromosome 6.

We constructed a metric linkage disequilibrium (LD) map of bovine chromosome 6 (BTA6) on the basis of data from 220 SNPs genotyped on 433 Australian dairy bulls. This metric LD map has distances in LD units (LDUs) that are analogous to centimorgans in linkage maps. The LD map of BTA6 has a total length of 8.9 LDUs. Within the LD map, regions of high LD (represented as blocks) and regions of low LD (steps) are observed, when plotted against the integrated map in kilobases. At the most stringent block definition, namely a set of loci with zero LDU increase over the span of these markers, BTA6 comprises 40 blocks, accounting for 41% of the chromosome. At a slightly lower stringency of block definition (a set of loci covering a maximum of 0.2 LDUs on the LD map), up to 81% of BTA6 is spanned by 46 blocks and with 13 steps that are likely to reflect recombination hot spots. The mean swept radius (the distance over which LD is likely to be useful for mapping) is 13.3 Mb, confirming extensive LD in Holstein-Friesian dairy cattle, which makes such populations ideal for whole-genome association studies.

Animals↗

PubMed2004

Validation of alternative methods of data normalization in gene co-expression studies.

MOTIVATION: Clusters of genes encoding proteins with related functions, or in the same regulatory network, often exhibit expression patterns that are correlated over a large number of conditions. Protein associations and gene regulatory networks can be modelled from expression data. We address the question of which of several normalization methods is optimal prior to computing the correlation of the expression profiles between every pair of genes. RESULTS: We use gene expression data from five experiments with a total of 78 hybridizations and 23 diverse conditions. Nine methods of data normalization are explored based on all possible combinations of normalization techniques according to between and within gene and experiment variation. We compare the resulting empirical distribution of gene x gene correlations with the expectations and apply cross-validation to test the performance of each method in predicting accurate functional annotation. We conclude that normalization methods based on mixed-model equations are optimal.

Algorithms↗

PubMed2004

Gene expression profiling of the bovine gastrointestinal tract.

Basal gene expression levels across the bovine gastrointestinal tract (GI) were examined in an attempt to formulate genetic explanations for the differences in function that are known or thought to exist between the various regions. Gene expression along the tract was studied through the random sequencing of a total of 16 412 clones from seven tissue-specific cDNA libraries spanning its length. The expressed sequence tags (ESTs) within each library were clustered to reduce clone redundancy and obtain longer consensus sequences. BLASTN and BLASTX searches against the NCBI human RefSeq databases were used to find putative matches for the bovine sequences and gene ontology assignments were made. Notable similarities and differences in gene expression were observed among the various compartments of the GI tract of the bovine. Many of the prominent transcripts have yet to be reliably identified and the prominence of others may be worthy of further examination. This collection of ESTs represents an important resource for the future construction of a GI tract specific microarray for further gene expression studies.

Animals↗