Personal tools

MCL coexpression mm9:2396

From FANTOM5_SSTAR

Revision as of 18:24, 11 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Phase1 CAGE Peaks

 Short description
Mm9::chr4:129419477..129419512,-p2@Khdrbs1
Mm9::chr6:29998062..29998078,+p2@Nrf1
Mm9::chr8:108160490..108160512,+p2@Ctcf
Mm9::chrX:98469402..98469427,+p3@Med12


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0006355regulation of transcription, DNA-dependent0.00264962671142477
GO:0006351transcription, DNA-dependent0.00264962671142477
GO:0032774RNA biosynthetic process0.00264962671142477
GO:0045449regulation of transcription0.00264962671142477
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00264962671142477
GO:0006350transcription0.00264962671142477
GO:0010468regulation of gene expression0.00264962671142477
GO:0031323regulation of cellular metabolic process0.00264962671142477
GO:0019222regulation of metabolic process0.00264962671142477
GO:0016070RNA metabolic process0.00264962671142477
GO:0046831regulation of RNA export from nucleus0.00264962671142477
GO:0010467gene expression0.00493676572862241
GO:0003676nucleic acid binding0.00501317796555137
GO:0010216maintenance of DNA methylation0.00586084345170822
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00586084345170822
GO:0050794regulation of cellular process0.00726818264355437
GO:0003918DNA topoisomerase (ATP-hydrolyzing) activity0.00856950403349945
GO:0050789regulation of biological process0.00994081576642363
GO:0006349genetic imprinting0.010196033647745
GO:0009048dosage compensation, by inactivation of X chromosome0.010196033647745
GO:0003916DNA topoisomerase activity0.0109891901210296
GO:0006265DNA topological change0.0109891901210296
GO:0007549dosage compensation0.0109891901210296
GO:0065007biological regulation0.0109891901210296
GO:0005634nucleus0.0114538221230214
GO:0043283biopolymer metabolic process0.0124452804732688
GO:0046822regulation of nucleocytoplasmic transport0.0129420245574463
GO:0005070SH3/SH2 adaptor activity0.0140866333941102
GO:0006305DNA alkylation0.0140866333941102
GO:0006405RNA export from nucleus0.0140866333941102
GO:0006306DNA methylation0.0140866333941102
GO:0003677DNA binding0.0158713381875643
GO:0006304DNA modification0.0158755623720686
GO:0005515protein binding0.0174588127541724
GO:0000119mediator complex0.0174588127541724
GO:0051168nuclear export0.0185873464027477
GO:0030674protein binding, bridging0.0196543615796995
GO:0006259DNA metabolic process0.0223176074557033
GO:0043170macromolecule metabolic process0.0247191938869611
GO:0007049cell cycle0.0275956870726719
GO:0043414biopolymer methylation0.0297006816389028
GO:0040029regulation of gene expression, epigenetic0.0297006816389028
GO:0060090molecular adaptor activity0.0297006816389028
GO:0032259methylation0.0297006816389028
GO:0050658RNA transport0.0301391412602402
GO:0051236establishment of RNA localization0.0301391412602402
GO:0016591DNA-directed RNA polymerase II, holoenzyme0.0301391412602402
GO:0050657nucleic acid transport0.0301391412602402
GO:0006403RNA localization0.0301391412602402
GO:0048523negative regulation of cellular process0.0301391412602402
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0312926256970316
GO:0044238primary metabolic process0.0318401864703
GO:0048519negative regulation of biological process0.0318401864703
GO:0044237cellular metabolic process0.0318401864703
GO:0043231intracellular membrane-bound organelle0.0318401864703
GO:0043227membrane-bound organelle0.0318401864703
GO:0003713transcription coactivator activity0.0345795460137525
GO:0006730one-carbon compound metabolic process0.0384526715069959
GO:0051049regulation of transport0.0412136454567188
GO:0006913nucleocytoplasmic transport0.0441006895042575
GO:0051169nuclear transport0.0441006895042575
GO:0043229intracellular organelle0.0464795240315621
GO:0043226organelle0.0464795240315621



Relative expression of the co-expression cluster over median <br>Analyst:





Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
lymphocyte7.80e-0713
common lymphoid progenitor7.80e-0713


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs




JASPAR motifs


Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}