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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1977_peripheral_occipital_parietal_temporal_neuroblastoma_amygdala_brain
|full_id=C1977_peripheral_occipital_parietal_temporal_neuroblastoma_amygdala_brain
|id=C1977
|id=C1977

Revision as of 14:37, 12 September 2012


Full id: C1977_peripheral_occipital_parietal_temporal_neuroblastoma_amygdala_brain



Phase1 CAGE Peaks

Hg19::chr6:40555143..40555161,-p2@LRFN2
Hg19::chr8:56014575..56014610,+p2@XKR4
Hg19::chr8:56014644..56014710,+p1@XKR4
Hg19::chr8:56015008..56015048,+p3@XKR4
Hg19::chr8:56025147..56025152,+p@chr8:56025147..56025152
+


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><br>

Cell Type
Ontology termp-valuen
neural cell1.48e-0725
neuronal stem cell4.54e-078
Uber Anatomy
Ontology termp-valuen
adult organism3.10e-57115
central nervous system5.92e-4682
regional part of nervous system2.42e-4594
nervous system2.42e-4594
neural tube1.23e-4157
neural rod1.23e-4157
future spinal cord1.23e-4157
neural keel1.23e-4157
neurectoderm1.65e-4190
neural plate7.20e-4086
presumptive neural plate7.20e-4086
brain3.34e-3669
future brain3.34e-3669
regional part of brain5.71e-3559
regional part of forebrain1.53e-3441
forebrain1.53e-3441
future forebrain1.53e-3441
anterior neural tube2.84e-3342
ectoderm1.36e-31173
presumptive ectoderm1.36e-31173
pre-chordal neural plate5.96e-3161
ectoderm-derived structure5.17e-30169
gray matter4.04e-2934
brain grey matter4.04e-2934
telencephalon4.04e-2934
regional part of telencephalon3.29e-2833
cerebral hemisphere5.33e-2832
anterior region of body2.78e-25129
craniocervical region2.78e-25129
head5.53e-24123
cerebral cortex1.99e-2225
pallium1.99e-2225
regional part of cerebral cortex1.34e-2122
neocortex7.88e-2020
organ part3.43e-11219
posterior neural tube1.87e-0915
chordal neural plate1.87e-0915
tube5.04e-09194
basal ganglion2.02e-089
nuclear complex of neuraxis2.02e-089
aggregate regional part of brain2.02e-089
collection of basal ganglia2.02e-089
cerebral subcortex2.02e-089
temporal lobe2.31e-087
nucleus of brain4.16e-089
neural nucleus4.16e-089
segmental subdivision of nervous system1.06e-0713
embryo1.65e-07612
segmental subdivision of hindbrain3.01e-0712
hindbrain3.01e-0712
presumptive hindbrain3.01e-0712
gyrus5.78e-076
anatomical conduit7.58e-07241
anatomical cluster8.75e-07286
diencephalon8.86e-077
future diencephalon8.86e-077


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
JUN#372537.50769751540180.004511206552906030.0213381295823801
REST#597835.790017229676810.009468788694433940.0357059078010538
ZNF263#1012746.577473309608540.0009875103237900160.00709511493576675



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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