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Coexpression cluster:C1991: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00111012223121416!ZNF263#10127;4:6.57747330960854:0.000987510323790016:0.00709560307576921
|tf_chipseq_enrich=EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00111012223121416!ZNF263#10127;4:6.57747330960854:0.000987510323790016:0.00709560307576921
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}}
}}

Revision as of 15:14, 26 November 2012


Full id: C1991_small_extraskeletal_non_acute_lymphoma_neuroblastoma_pineal



Phase1 CAGE Peaks

Hg19::chr7:18535346..18535399,+p1@HDAC9
Hg19::chr7:18535786..18535808,+p12@HDAC9
Hg19::chr7:18535844..18535853,+p35@HDAC9
Hg19::chr7:18535854..18535890,+p8@HDAC9
Hg19::chr7:18535893..18535918,+p10@HDAC9


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 cell1.60e-1025
neuronal stem cell1.61e-078
Uber Anatomy
Ontology termp-valuen
nervous system5.81e-3989
central nervous system4.13e-3881
neural tube2.93e-3556
neural rod2.93e-3556
future spinal cord2.93e-3556
neural keel2.93e-3556
regional part of nervous system1.46e-3353
regional part of brain1.46e-3353
adult organism2.02e-30114
regional part of forebrain3.94e-2941
forebrain3.94e-2941
anterior neural tube3.94e-2941
future forebrain3.94e-2941
brain4.01e-2968
future brain4.01e-2968
neural plate7.83e-2782
presumptive neural plate7.83e-2782
neurectoderm5.48e-2686
telencephalon3.74e-2534
brain grey matter1.81e-2434
gray matter1.81e-2434
cerebral hemisphere5.25e-2432
regional part of telencephalon1.68e-2332
cerebral cortex6.19e-2325
pallium6.19e-2325
ectoderm-derived structure5.82e-22171
ectoderm5.82e-22171
presumptive ectoderm5.82e-22171
pre-chordal neural plate1.36e-2161
ecto-epithelium5.41e-21104
regional part of cerebral cortex5.02e-2022
neocortex1.93e-1820
structure with developmental contribution from neural crest1.16e-16132
organ system subdivision4.89e-15223
posterior neural tube1.64e-0715
chordal neural plate1.64e-0715
gyrus6.62e-076
tube7.14e-07192
anatomical cluster8.26e-07373


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
EP300#203356.77394172622327.00901578206049e-050.00111012223121416
ZNF263#1012746.577473309608540.0009875103237900160.00709560307576921



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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