We are analyzing https://link.springer.com/article/10.1186/1471-2164-5-4.

Title:
Inter-species differences of co-expression of neighboring genes in eukaryotic genomes | BMC Genomics
Description:
Background There is increasing evidence that gene order within the eukaryotic genome is not random. In yeast and worm, adjacent or neighboring genes tend to be co-expressed. Clustering of co-expressed genes has been found in humans, worm and fruit flies. However, in mice and rats, an effect of chromosomal distance (CD) on co-expression has not been investigated yet. Also, no cross-species comparison has been made so far. We analyzed the effect of CD as well as normalized distance (ND) using expression data in six eukaryotic species: yeast, fruit fly, worm, rat, mouse and human. Results We analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8 – 30 % of the highly co-expressed pairs are duplic ated genes. Conclusion We confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD.
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Keywords {🔍}

pairs, genes, article, pubmed, worm, species, expression, google, scholar, coexpression, distance, gene, yeast, results, cas, datasets, analysis, human, coer, coers, effect, kbp, data, genome, mouse, table, comparison, pga, information, differences, neighboring, eukaryotic, range, chromosomal, fig, interspecies, coexpressed, fruit, rat, nature, obtained, blast, dataset, authors, access, full, normalized, fly, eleven, protein,

Topics {✒️}

org/tigr-scripts/magic/r1 pair-wise protein blast genome-wide expression patterns open access license article download pdf bell-shaped curve centered uk/projects/c_elegans/wormpep/ genome-wide microarray analysis pga human cd4+lymphocytes /groups/proj1/pages/swim_home full size image embryonic nervous system bmc genomics 5 gene expression profiling full access pair-wise analysis genome-wide analysis protein blast analysis related subjects investigated inter-species differences cross-species comparison pair-wised blast authors’ original file privacy choices/manage cookies investigate intra-species differences coordinated gene regulation article fukuoka inter-species comparison inter-species differences significant intra-species difference context-dependent transcription inter-species comparisons dna sequencing activities genome oligonucleotide arrays glial cells missing author information authors pair-wise pearson correlation coefficient european economic area equal sized intervals intrachromosomal colocalization strengthens expression profiles combined gov/genbank/genomes/ /maps/lk/gnomap/ complicated functional relationships unic ellular eukaryote specific enhancer activity genetic selections exercise induced hypertrophy den boer ml

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         headline:Inter-species differences of co-expression of neighboring genes in eukaryotic genomes
         description:There is increasing evidence that gene order within the eukaryotic genome is not random. In yeast and worm, adjacent or neighboring genes tend to be co-expressed. Clustering of co-expressed genes has been found in humans, worm and fruit flies. However, in mice and rats, an effect of chromosomal distance (CD) on co-expression has not been investigated yet. Also, no cross-species comparison has been made so far. We analyzed the effect of CD as well as normalized distance (ND) using expression data in six eukaryotic species: yeast, fruit fly, worm, rat, mouse and human. We analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8 – 30 % of the highly co-expressed pairs are duplic ated genes. We confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD.
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      headline:Inter-species differences of co-expression of neighboring genes in eukaryotic genomes
      description:There is increasing evidence that gene order within the eukaryotic genome is not random. In yeast and worm, adjacent or neighboring genes tend to be co-expressed. Clustering of co-expressed genes has been found in humans, worm and fruit flies. However, in mice and rats, an effect of chromosomal distance (CD) on co-expression has not been investigated yet. Also, no cross-species comparison has been made so far. We analyzed the effect of CD as well as normalized distance (ND) using expression data in six eukaryotic species: yeast, fruit fly, worm, rat, mouse and human. We analyzed 24 sets of expression data from the six species. Highly co-expressed pairs were sorted into bins of equal sized intervals of CD, and a co-expression rate (CoER) in each bin was calculated. In all datasets, a higher CoER was obtained in a short CD range than a long distance range. These results show that across all studied species, there was a consistent effect of CD on co-expression. However, the results using the ND show more diversity. Intra- and inter-species comparisons of CoER reveal that there are significant differences in the co-expression rates of neighboring genes among the species. A pair-wise BLAST analysis finds 8 – 30 % of the highly co-expressed pairs are duplic ated genes. We confirmed that in the six eukaryotic species, there was a consistent tendency that neighboring genes are likely to be co-expressed. Results of pair-wised BLAST indicate a significant effect of non-duplicated pairs on co-expression. A comparison of CD and ND suggests the dominant effect of CD.
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         inter-species comparison
         chromosomal distance
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         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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