Gene Expression Regulation via Pluripotency Related Transcription Factors and Micro RNA in Mouse Embryonic Stem Cell during Differentiation Y-h. Tahguchi,

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Gene Expression Regulation via Pluripotency Related Transcription Factors and Micro RNA in Mouse Embryonic Stem Cell during Differentiation Y-h. Tahguchi, Dept. Phys., Chuo Univ., Paul Bertone, EBI, EMBL.

genome gene TF2TF1 mRNA miRNA1miRNA2 ESES lineages time Gene exp. up dow n TF1TF2 miRNA 1 miRNA 2 gene1 °£°° gene2 £°°£ gene3 °£££ gene4 ££££ at ES cell (known) Comp. Pred. binding Target

Gene expression Embedding (2D) Each dot = gene expression Principal component analysis ES Biological replicates 1 and 2 1 st PC Up Down regulation TF1TF2TF3TF4miR NA1 miR NA2 miR NA3 miR NA4 miR NA5 gene gene gene gene gene gene gene gene gene Hypergeometric analysis Mean of gene 2 and 4

Results For TF binding;  Many TF binding combinations result in significant P-value (P<0.05).  More TF bindings causes downregulation.  Regulation by TF binding is weakly lineage specific.  TF binding is stochastic decreasing process during differentiation.

PC1 by other kind of PCA. Numbers : time order Color : lineages Regulation by TF binding is weakly lineage specific. Less TFbindings

For TF bindings + miRNA target  No miRNA target results in significant P-value (Exception, data from Anton group).  But mean FDR << 1, thus many true positives are hidden.  Regulation by miRNA target is strongly lineage specific.  More miRNAs target causes upregulation (mostly. Sometimes, downregulation, too).

More miRNAs target causes upregulation Time Color, number : Number of miRNAs which target each gene. Top 10 miRNAs used. Caution; This is “mean” gene expression and is deviation from “over all mean”. “Over all mean” is strongly downregulated due to TF bindings. Gene expression Anton group's data

Conclusion