Personal tools

Coexpression cluster:C2296

From FANTOM5_SSTAR

Revision as of 15:24, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2296_pineal_temporal_occipital_parietal_duodenum_spinal_optic



Phase1 CAGE Peaks

Hg19::chr14:48006773..48006777,-p@chr14:48006773..48006777
-
Hg19::chr14:48144799..48144820,-p@chr14:48144799..48144820
-
Hg19::chr1:178340501..178340532,+p@chr1:178340501..178340532
+
Hg19::chr4:165305086..165305179,-p2@MARCH1


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube8.46e-7056
neural rod8.46e-7056
future spinal cord8.46e-7056
neural keel8.46e-7056
central nervous system3.02e-6781
regional part of nervous system1.21e-6553
regional part of brain1.21e-6553
nervous system6.69e-6489
brain1.22e-5868
future brain1.22e-5868
neurectoderm6.26e-5886
neural plate2.21e-5682
presumptive neural plate2.21e-5682
regional part of forebrain2.58e-5441
forebrain2.58e-5441
anterior neural tube2.58e-5441
future forebrain2.58e-5441
pre-chordal neural plate5.99e-4761
brain grey matter1.60e-4534
gray matter1.60e-4534
telencephalon2.47e-4534
ecto-epithelium2.20e-44104
cerebral hemisphere3.72e-4332
regional part of telencephalon6.78e-4332
ectoderm-derived structure1.60e-39171
ectoderm1.60e-39171
presumptive ectoderm1.60e-39171
structure with developmental contribution from neural crest5.54e-37132
cerebral cortex3.83e-3425
pallium3.83e-3425
regional part of cerebral cortex3.84e-3222
adult organism9.74e-31114
neocortex1.14e-2920
organ system subdivision4.64e-27223
posterior neural tube5.15e-1615
chordal neural plate5.15e-1615
segmental subdivision of nervous system2.11e-1313
anatomical cluster2.63e-13373
tube5.80e-13192
basal ganglion1.07e-129
nuclear complex of neuraxis1.07e-129
aggregate regional part of brain1.07e-129
collection of basal ganglia1.07e-129
cerebral subcortex1.07e-129
neural nucleus1.25e-129
nucleus of brain1.25e-129
segmental subdivision of hindbrain2.88e-1212
hindbrain2.88e-1212
presumptive hindbrain2.88e-1212
temporal lobe1.21e-106
diencephalon3.63e-107
future diencephalon3.63e-107
telencephalic nucleus4.11e-107
multi-tissue structure1.03e-09342
gyrus1.07e-096
organ part1.33e-09218
anatomical conduit4.78e-09240
brainstem6.01e-096
regional part of metencephalon7.31e-099
metencephalon7.31e-099
future metencephalon7.31e-099
occipital lobe1.80e-085
parietal lobe2.47e-085
epithelium2.79e-08306
cell layer5.23e-08309
limbic system5.98e-085
embryo2.99e-07592
regional part of diencephalon7.65e-074
gland of diencephalon8.82e-074
neuroendocrine gland8.82e-074
corpus striatum9.08e-074
striatum9.08e-074
ventral part of telencephalon9.08e-074
future corpus striatum9.08e-074


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
CTBP2#1488231.35850016966410.001492676882047230.00953886562345534



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.