Open Access Research article

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach

Jun Odawara12, Akihito Harada1, Tomohiko Yoshimi3, Kazumitsu Maehara1, Taro Tachibana3, Seiji Okada1, Koichi Akashi2 and Yasuyuki Ohkawa1*

Author Affiliations

1 Faculty of Medicine Div. Epigenetics, Kyushu University, Fukuoka 812-8582, Japan

2 Department of Medicine and Biosystemic Sciences, Kyushu University Graduate School of Medicine, Fukuoka 812-8582, Japan

3 Department of Bioengineering, Graduate School of Engineering, Osaka City University, Osaka 558-8585, Japan

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BMC Genomics 2011, 12:516  doi:10.1186/1471-2164-12-516

Published: 20 October 2011

Additional files

Additional file 1:

Supplementary Figure S1. mRNA expressions of representative genes whose FPKM values were low. Their expressions could be confirmed by PCR. We chose the low FPKM value genes at random from the group in which the existence of phosphorylated RNAPII could not be confirmed by ChIPseq.

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Additional file 2:

Supplementary Figure S2. (a) Venn diagram summarizing the overlap between FPKM > 0 genes, Ser2P genes, and Ser5P genes according the 'Max multihits' parameter. (b) A line graph showing how many detected genes increase in each category when 'Max multihits' parameter increases from 1. Both (a) and (b) indicated that when 'Max multihits' parameter increases, the number of genes detected by RNAseq rises, mainly in the group RNAseq(+), Ser2P(-), Ser5P(-).

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Additional file 3:

Supplementary Table S1. Significant GO terms for each category. To investigate the functional relationship among pausing/active genes and gene functions, we analyzed significant association using Gene ontology and Fishers' exact test. Though hundreds of GO terms were judged to be significant for double positive (RNAseq+/-, Ser2P+m Ser5P+) genes, for the other categories, significant GO terms were merely found.

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Additional file 4:

Supplementary Figure S3. Relative tags from FPKM > 0/Ser2P(+)/Ser5P(-) genes in ChIPseq indicate their source as background noise. When Ser5P (a) and Ser2P (b) tags were summed for genes with FPKM > 0/Ser2P(+)/Ser5P(-), the tag count outside of the gene was higher than for other gene categories. This may indicate that they were picked up from the background noise generated by surrounding genes.

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