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Coexpression cluster:C3335

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Full id: C3335_maxillary_acute_merkel_medial_small_pineal_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:79611273..79611298,+p15@SYT1
Hg19::chr5:139064793..139064798,+p@chr5:139064793..139064798
+
Hg19::chr5:139064799..139064811,+p@chr5:139064799..139064811
+


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
ciliated cell2.45e-073
multi-ciliated epithelial cell2.45e-073
ciliated epithelial cell2.45e-073
non-pigmented ciliary epithelial cell2.45e-073
Uber Anatomy
Ontology termp-valuen
neural tube1.82e-4557
neural rod1.82e-4557
future spinal cord1.82e-4557
neural keel1.82e-4557
regional part of nervous system3.95e-4194
nervous system3.95e-4194
regional part of brain8.48e-4159
central nervous system2.15e-4082
neural plate2.32e-4086
presumptive neural plate2.32e-4086
neurectoderm5.30e-4090
brain7.70e-4069
future brain7.70e-4069
regional part of forebrain4.57e-3941
forebrain4.57e-3941
future forebrain4.57e-3941
anterior neural tube5.83e-3842
cerebral hemisphere2.98e-3732
pre-chordal neural plate1.21e-3661
telencephalon1.04e-3434
gray matter1.05e-3434
brain grey matter1.05e-3434
regional part of telencephalon5.22e-3333
regional part of cerebral cortex9.10e-3222
head1.06e-30123
cerebral cortex1.64e-3025
pallium1.64e-3025
anterior region of body2.15e-30129
craniocervical region2.15e-30129
neocortex2.71e-2720
ectoderm2.88e-26173
presumptive ectoderm2.88e-26173
ectoderm-derived structure5.53e-26169
adult organism1.55e-20115
gyrus2.82e-156
tube6.39e-11194
organ part1.66e-10219
epithelium8.23e-10309
cell layer1.36e-09312
organism subdivision4.10e-09365
posterior neural tube6.98e-0915
chordal neural plate6.98e-0915
middle temporal gyrus7.45e-093
segmental subdivision of hindbrain1.13e-0812
hindbrain1.13e-0812
presumptive hindbrain1.13e-0812
parietal lobe1.52e-085
limbic system2.11e-085
occipital lobe2.71e-085
segmental subdivision of nervous system6.33e-0813
anatomical cluster9.92e-08286
temporal lobe1.11e-077
anatomical conduit1.99e-07241
ciliary epithelium2.45e-073
ciliary body2.45e-073
Disease
Ontology termp-valuen
bronchus cancer1.33e-087
bronchogenic carcinoma1.33e-087


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
NR3C1#290829.982015554115360.01278474365547170.0460216400452835



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.