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Coexpression cluster:C2777: Difference between revisions

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|tf_chipseq_enrich=FOXA1#3169;3:8.31106481203909:0.00274013818210985:0.0150405892469317!FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353514055585333
|tf_chipseq_enrich=FOXA1#3169;3:8.31106481203909:0.00274013818210985:0.0150405892469317!FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353514055585333
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}}
}}

Revision as of 15:42, 26 November 2012


Full id: C2777_medulloblastoma_occipital_temporal_parietal_duodenum_neuroblastoma_Neurons



Phase1 CAGE Peaks

Hg19::chr4:140478299..140478335,-p5@SETD7
Hg19::chr4:186877481..186877494,-p18@SORBS2
Hg19::chr9:103791052..103791084,+p3@LPPR1
Hg19::chr9:103791098..103791109,+p9@LPPR1


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:0018024histone-lysine N-methyltransferase activity0.0181391123449527
GO:0016278lysine N-methyltransferase activity0.0181391123449527
GO:0016279protein-lysine N-methyltransferase activity0.0181391123449527
GO:0042054histone methyltransferase activity0.0181391123449527
GO:0008276protein methyltransferase activity0.0181391123449527
GO:0008170N-methyltransferase activity0.0181391123449527
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0267280542339939



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
neuronal stem cell4.60e-078
Uber Anatomy
Ontology termp-valuen
nervous system1.53e-6389
central nervous system1.97e-6381
neural tube3.26e-6156
neural rod3.26e-6156
future spinal cord3.26e-6156
neural keel3.26e-6156
regional part of nervous system4.37e-5753
regional part of brain4.37e-5753
regional part of forebrain8.82e-5341
forebrain8.82e-5341
anterior neural tube8.82e-5341
future forebrain8.82e-5341
brain5.92e-5168
future brain5.92e-5168
neural plate2.03e-4882
presumptive neural plate2.03e-4882
neurectoderm5.12e-4786
telencephalon4.91e-4634
brain grey matter5.78e-4634
gray matter5.78e-4634
cerebral hemisphere1.52e-4332
regional part of telencephalon2.16e-4332
pre-chordal neural plate3.85e-4061
ecto-epithelium8.97e-39104
adult organism1.46e-37114
cerebral cortex6.56e-3425
pallium6.56e-3425
ectoderm-derived structure2.75e-33171
ectoderm2.75e-33171
presumptive ectoderm2.75e-33171
organ system subdivision4.90e-32223
regional part of cerebral cortex9.98e-3122
neocortex3.04e-2820
structure with developmental contribution from neural crest2.53e-27132
tube4.61e-18192
anatomical cluster4.65e-17373
basal ganglion1.01e-139
nuclear complex of neuraxis1.01e-139
aggregate regional part of brain1.01e-139
collection of basal ganglia1.01e-139
cerebral subcortex1.01e-139
anatomical conduit1.87e-13240
neural nucleus2.66e-139
nucleus of brain2.66e-139
telencephalic nucleus7.65e-117
posterior neural tube2.79e-1015
chordal neural plate2.79e-1015
epithelium2.80e-10306
cell layer5.55e-10309
gyrus6.39e-106
embryo2.02e-09592
brainstem4.42e-096
parietal lobe6.25e-095
temporal lobe1.29e-086
occipital lobe1.88e-085
limbic system1.96e-085
diencephalon4.14e-087
future diencephalon4.14e-087
germ layer4.33e-08560
germ layer / neural crest4.33e-08560
embryonic tissue4.33e-08560
presumptive structure4.33e-08560
germ layer / neural crest derived structure4.33e-08560
epiblast (generic)4.33e-08560
segmental subdivision of nervous system5.25e-0813
multi-tissue structure6.56e-08342
embryonic structure7.91e-08564
developing anatomical structure1.74e-07581
corpus striatum1.80e-074
striatum1.80e-074
ventral part of telencephalon1.80e-074
future corpus striatum1.80e-074
regional part of diencephalon4.30e-074
multi-cellular organism5.42e-07656
segmental subdivision of hindbrain6.51e-0712
hindbrain6.51e-0712
presumptive hindbrain6.51e-0712


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
FOXA1#316938.311064812039090.002740138182109850.0150405892469317
FOXA2#3170212.31523187633260.009361916285467240.0353514055585333



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.

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