Transcriptomics

Dataset Information

309

Gene expression profiling of 19 cattle tissues reveals unique patterns related to tissue function


ABSTRACT: cDNA microarrays have been shown to be useful for monitoring global gene expression patterns in normal and disease states and in response to various environmental stimuli. In this study we have used a cattle cDNA microarray containing 7653 elements to analyze expression profiles in 19 different cattle tissues. Signal intensities from all tissue sample RNAs were compared to a reference standard RNA created from different tissues and cell lines. Data analysis identified a subset of genes significantly differentially expressed between tissues and the reference standard that were further subdivided according to fold change. Log transformed ratios were normalized using the intensity-based regional Lowess algorithm. A global error model, to account for the dependence of variation on signal intensities, was used to identify lists of genes for effect of tissue on gene expression taking into account an experiment-wise significance of 0.05, using either a Bonferroni correction (663 genes) or Benjamini and Hochberg’s False Discovery Rate (3350 genes). Non-supervised cluster analysis revealed groups of genes common to nerve, muscle, immune or digestive tissues. Discriminant analysis was used to support physiological functional categories and embryonic origin of tissues. Unique profiles were constructed with genes preferentially expressed in specific tissues or tissue groups in order to define gene expression for individual tissues. Global expression along a large collection of tissues revealed tissue specific expression of enzyme isomers and utilization in specific metabolic pathways. A comprehensive matrix of all possible pair-wise comparisons for individual genes among tissues was constructed to further identify genes with tissue-specific behavior and possibly unique function. A reference design was used to compare 19 cattle tissues. All tissues were compared to a universal control consisting of a mix of cattle cell lines. All samples were duplicated with a dye swap.

ORGANISM(S): Bos taurus  

SUBMITTER: Robin E Everts   Sandra L Rodriguez-Zas  Mark R Band  Dawn E Morin  Harris A Lewin  Mark Robert Band  Zonglin L Liu  Jonathan U Peled 

PROVIDER: E-GEOD-3029 | ArrayExpress | 2010-07-01

SECONDARY ACCESSION(S): GSE3029PRJNA93015

REPOSITORIES: GEO, ArrayExpress

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Publications

Discovery of eight novel divergent homologs expressed in cattle placenta.

Larson Joshua H JH   Kumar Charu G CG   Everts Robin E RE   Green Cheryl A CA   Everts-van der Wind Annelie A   Band Mark R MR   Lewin Harris A HA  

Physiological genomics 20060322 3


Ten divergent homologs were identified using a subtractive bioinformatic analysis of 12,614 cattle placenta expressed sequence tags followed by comparative, evolutionary, and gene expression studies. Among the 10 divergent homologs, 8 have not been identified previously. These were named as follows: cattle cerebrum and skeletal muscle-specific transcript 1 (CSSMST1), cattle intestine-specific transcript 1 (CIST1), hepatitis A virus cellular receptor 1 amino-terminal domain-containing protein (HA  ...[more]

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