Personal tools

Coexpression cluster:C798

From FANTOM5_SSTAR

Revision as of 16:43, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C798_cerebellum_small_carcinosarcoma_argyrophil_Neural_gastric_Ciliary



Phase1 CAGE Peaks

Hg19::chr11:31816236..31816261,-p@chr11:31816236..31816261
-
Hg19::chr11:31816304..31816311,-p@chr11:31816304..31816311
-
Hg19::chr11:31819053..31819055,-p@chr11:31819053..31819055
-
Hg19::chr11:31832581..31832601,-p7@PAX6
Hg19::chr11:31832610..31832639,-p5@PAX6
Hg19::chr11:31832658..31832681,-p1@PAX6
Hg19::chr11:31832687..31832704,-p6@PAX6
Hg19::chr11:31832807..31832823,-p4@PAX6
Hg19::chr11:31832862..31832884,-p2@PAX6
Hg19::chr11:31833011..31833025,+p@chr11:31833011..31833025
+


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


No GOStat results

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>disease_data<br>


Cell Type
Ontology termp-valuen
oligodendrocyte5.07e-097
macroglial cell5.07e-097
astrocyte5.07e-097
oligodendrocyte precursor cell5.07e-097
neural cell1.48e-0825
Uber Anatomy
Ontology termp-valuen
neurectoderm4.89e-5586
neural plate1.25e-5382
presumptive neural plate1.25e-5382
neural tube1.78e-5056
neural rod1.78e-5056
future spinal cord1.78e-5056
neural keel1.78e-5056
nervous system4.76e-4789
regional part of nervous system5.80e-4753
regional part of brain5.80e-4753
central nervous system7.87e-4781
pre-chordal neural plate3.13e-4361
ecto-epithelium2.52e-40104
brain3.67e-4068
future brain3.67e-4068
regional part of forebrain4.13e-3441
forebrain4.13e-3441
anterior neural tube4.13e-3441
future forebrain4.13e-3441
ectoderm-derived structure8.56e-33171
ectoderm8.56e-33171
presumptive ectoderm8.56e-33171
brain grey matter2.50e-2934
gray matter2.50e-2934
telencephalon2.58e-2934
structure with developmental contribution from neural crest1.63e-28132
cerebral hemisphere1.58e-2732
regional part of telencephalon1.83e-2732
cerebral cortex2.81e-2125
pallium2.81e-2125
organ system subdivision4.72e-18223
regional part of cerebral cortex8.36e-1822
posterior neural tube3.06e-1715
chordal neural plate3.06e-1715
neocortex1.04e-1520
segmental subdivision of hindbrain6.50e-1412
hindbrain6.50e-1412
presumptive hindbrain6.50e-1412
pigment epithelium of eye7.90e-1411
segmental subdivision of nervous system1.51e-1213
adult organism4.81e-12114
eye1.74e-1121
visual system1.74e-1121
anatomical cluster4.52e-11373
regional part of metencephalon1.02e-109
metencephalon1.02e-109
future metencephalon1.02e-109
camera-type eye2.05e-1020
simple eye2.05e-1020
immature eye2.05e-1020
ocular region2.05e-1020
eyeball of camera-type eye2.05e-1020
optic cup2.05e-1020
optic vesicle2.05e-1020
eye primordium2.05e-1020
basal ganglion1.44e-099
nuclear complex of neuraxis1.44e-099
aggregate regional part of brain1.44e-099
collection of basal ganglia1.44e-099
cerebral subcortex1.44e-099
neural nucleus1.76e-099
nucleus of brain1.76e-099
sense organ1.94e-0924
sensory system1.94e-0924
entire sense organ system1.94e-0924
face4.59e-0922
organ part4.69e-09218
cerebellum2.73e-086
rhombic lip2.73e-086
anterior segment of eyeball2.98e-0814
tube9.70e-08192
telencephalic nucleus1.15e-077
epithelium2.12e-07306
brainstem2.84e-076
cell layer3.94e-07309
Disease
Ontology termp-valuen
cell type cancer8.86e-12143
disease of cellular proliferation5.16e-07239
cancer7.84e-07235


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
CCNT2#90574.435341103873840.0001875292697571890.00226735001205963
CEBPB#105175.579803338077374.14051761029175e-050.000751532010255926
CTBP2#1488743.90190023752972.99349477998484e-113.4698956862024e-09
E2F4#187478.867642220699111.84731179412716e-066.85369081587377e-05
E2F6#187673.512009012188170.0008453950419482970.00637258843637951
ELF1#199772.980668571165280.002378202870469130.0134731288087294
FOS#235376.298568716226081.848304348188e-050.00041991528784078
HDAC2#306668.049372141975762.76518202234458e-050.000584600901278635
JUND#372774.896264759309729.81446965345405e-050.00139173577208023
MAX#414974.516788856304990.0001665254509713970.00204152501162128
NANOG#79923720.47134493670895.96944508093541e-094.74101045481227e-07
NFYA#4800712.89790648988141.4357468212053e-078.1272608270927e-06
NFYB#4801711.73185527747552.74641977103244e-071.40950041507055e-05
POU2F2#545276.374286840419771.70647444265859e-050.000390838781396536
SPI1#668875.743026455965913.41922598863134e-050.00067825364297563
SUZ12#23512735.0810466377441.42572395471382e-101.51322341571501e-08
TAF1#687272.34013240002170.01040839844348330.0386352973073269
TBP#690872.594739480967470.00558866901773640.0252727864708107
TRIM28#10155713.01336753168381.35067750650695e-077.68737918812423e-06
ZNF263#1012775.755289145907473.37110736015453e-050.000669217033999579



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.