Personal tools

Coexpression cluster:C699

From FANTOM5_SSTAR

Revision as of 12:51, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C699_medulloblastoma_Lens_neuroblastoma_Ciliary_eye_small_cerebellum



Phase1 CAGE Peaks

Hg19::chr13:36045322..36045356,+p9@NBEA
Hg19::chr13:36046061..36046077,+p@chr13:36046061..36046077
+
Hg19::chr13:36046127..36046134,+p@chr13:36046127..36046134
+
Hg19::chr13:36046521..36046554,+p@chr13:36046521..36046554
+
Hg19::chr13:36050790..36050807,-p2@MAB21L1
Hg19::chr13:36050819..36050834,-p1@MAB21L1
Hg19::chr13:36050881..36050887,+p3@NBEA
Hg19::chr13:36050940..36050952,+p2@NBEA
Hg19::chr13:36050956..36050969,+p4@NBEA
Hg19::chr13:36050976..36050990,+p8@NBEA
Hg19::chr13:36052762..36052767,-p@chr13:36052762..36052767
-
Hg19::chr13:36052779..36052793,-p@chr13:36052779..36052793
-


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


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


GO IDGO nameFDR corrected p-value
GO:0005802trans-Golgi network0.0296627598117251



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
non-terminally differentiated cell6.95e-16180
fibroblast1.10e-1375
stuff accumulating cell2.18e-0939
skin fibroblast7.51e-0923
fat cell1.58e-0715
Uber Anatomy
Ontology termp-valuen
anterior region of body6.90e-24129
craniocervical region6.90e-24129
head8.91e-24123
ectoderm-derived structure3.92e-23169
neural plate4.26e-2386
presumptive neural plate4.26e-2386
ectoderm1.17e-22173
presumptive ectoderm1.17e-22173
neurectoderm4.00e-2290
organism subdivision1.84e-20365
regional part of nervous system1.44e-1894
nervous system1.44e-1894
pre-chordal neural plate1.33e-1661
neural tube1.49e-1657
neural rod1.49e-1657
future spinal cord1.49e-1657
neural keel1.49e-1657
regional part of brain7.44e-1559
central nervous system8.74e-1582
brain9.90e-1469
future brain9.90e-1469
adult organism1.86e-13115
subdivision of head6.55e-1348
surface structure3.04e-1195
face6.36e-1021
eye9.18e-1020
sense organ1.38e-0923
posterior neural tube1.66e-0915
chordal neural plate1.66e-0915
anterior neural tube2.35e-0942
camera-type eye4.99e-0919
simple eye4.99e-0919
ocular region4.99e-0919
optic cup4.99e-0919
eye primordium4.99e-0919
optic vesicle4.99e-0919
visual system6.78e-0921
multi-tissue structure7.16e-09347
regional part of forebrain7.92e-0941
forebrain7.92e-0941
future forebrain7.92e-0941
sensory system8.28e-0924
entire sense organ system8.28e-0924
gray matter7.50e-0834
brain grey matter7.50e-0834
pigment epithelium of eye8.26e-0811
segmental subdivision of hindbrain1.03e-0712
hindbrain1.03e-0712
presumptive hindbrain1.03e-0712
integument2.16e-0745
integumental system2.16e-0745
cell layer2.40e-07312
telencephalon4.41e-0734
regional part of telencephalon5.11e-0733
somite5.54e-0783
paraxial mesoderm5.54e-0783
presomitic mesoderm5.54e-0783
presumptive segmental plate5.54e-0783
trunk paraxial mesoderm5.54e-0783
presumptive paraxial mesoderm5.54e-0783
ectodermal placode8.54e-0729
cerebral hemisphere9.98e-0732


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
REST#597875.629183417741356.32358000930756e-050.00103224190777129
SUZ12#235121250.11578091106293.91454139263279e-211.04293568496218e-18



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.