Personal tools

MCL coexpression mm9:470

From FANTOM5_SSTAR

Revision as of 20:44, 11 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Phase1 CAGE Peaks

 Short description
Mm9::chr19:59245978..59245982,-p1@Vax1
Mm9::chr2:157385838..157385855,+p1@Nnat
Mm9::chr2:157387453..157387467,+p@chr2:157387453..157387467
+
Mm9::chr2:157387508..157387519,+p@chr2:157387508..157387519
+
Mm9::chr2:157387588..157387620,-p@chr2:157387588..157387620
-
Mm9::chr2:157387609..157387632,+p@chr2:157387609..157387632
+
Mm9::chr2:157387638..157387650,+p@chr2:157387638..157387650
+
Mm9::chr2:157387715..157387750,-p@chr2:157387715..157387750
-
Mm9::chr2:157387765..157387768,+p@chr2:157387765..157387768
+
Mm9::chr2:157387844..157387880,+p@chr2:157387844..157387880
+
Mm9::chr2:157387891..157387954,+p@chr2:157387891..157387954
+
Mm9::chr2:157388016..157388027,+p@chr2:157388016..157388027
+
Mm9::chr2:157388030..157388056,+p@chr2:157388030..157388056
+
Mm9::chr2:162948341..162948356,+p1@ENSMUST00000144092
Mm9::chr2:31495237..31495243,+p1@Prdm12
Mm9::chr4:128905127..128905167,-p3@C77080


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:0031490chromatin DNA binding0.0335241425283526
GO:0007406negative regulation of neuroblast proliferation0.0335241425283526



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>


Uber Anatomy
Ontology termp-valuen
neurectoderm1.55e-1764
neural plate1.55e-1764
presumptive neural plate1.55e-1764
central nervous system2.58e-1773
regional part of nervous system3.88e-1754
ectoderm-derived structure1.33e-1695
ectoderm1.33e-1695
presumptive ectoderm1.33e-1695
nervous system2.48e-1675
neural tube1.54e-1552
neural rod1.54e-1552
future spinal cord1.54e-1552
neural keel1.54e-1552
ecto-epithelium4.86e-1573
pre-chordal neural plate1.34e-1449
brain2.64e-1247
future brain2.64e-1247
regional part of brain6.47e-1246
anterior neural tube6.70e-1240
regional part of forebrain9.80e-1239
forebrain9.80e-1239
future forebrain9.80e-1239
structure with developmental contribution from neural crest1.32e-1192
diencephalon1.53e-0910
future diencephalon1.53e-0910
pituitary gland1.29e-088
gland of diencephalon1.29e-088
neuroendocrine gland1.29e-088
gray matter3.03e-0834
basal ganglion4.56e-078
nuclear complex of neuraxis4.56e-078
aggregate regional part of brain4.56e-078
collection of basal ganglia4.56e-078
cerebral subcortex4.56e-078


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}}}