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Coexpression cluster:C1628: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239217248041853!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386503557940323!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135132457389314
|tf_chipseq_enrich=CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239217248041853!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386503557940323!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135132457389314
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}}
}}

Revision as of 15:00, 26 November 2012


Full id: C1628_mesodermal_spinal_locus_parietal_temporal_medulla_thalamus



Phase1 CAGE Peaks

Hg19::chr11:24518511..24518530,+p6@LUZP2
Hg19::chr11:24518538..24518620,+p1@LUZP2
Hg19::chr11:24518633..24518649,+p4@LUZP2
Hg19::chr11:24518654..24518698,+p2@LUZP2
Hg19::chr11:24518723..24518745,+p7@LUZP2


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
neuronal stem cell1.52e-088
Uber Anatomy
Ontology termp-valuen
central nervous system2.20e-6581
neural tube4.35e-6456
neural rod4.35e-6456
future spinal cord4.35e-6456
neural keel4.35e-6456
nervous system2.68e-6389
regional part of nervous system8.49e-5953
regional part of brain8.49e-5953
regional part of forebrain1.16e-5141
forebrain1.16e-5141
anterior neural tube1.16e-5141
future forebrain1.16e-5141
brain3.28e-5068
future brain3.28e-5068
neural plate1.68e-4982
presumptive neural plate1.68e-4982
neurectoderm2.29e-4686
brain grey matter4.58e-4234
gray matter4.58e-4234
pre-chordal neural plate6.52e-4261
telencephalon1.17e-4134
regional part of telencephalon1.20e-3832
cerebral hemisphere1.47e-3832
ecto-epithelium2.71e-38104
adult organism5.70e-37114
ectoderm-derived structure3.81e-34171
ectoderm3.81e-34171
presumptive ectoderm3.81e-34171
structure with developmental contribution from neural crest7.27e-34132
regional part of cerebral cortex1.24e-3222
organ system subdivision6.35e-30223
neocortex2.05e-2920
cerebral cortex5.49e-2825
pallium5.49e-2825
neural nucleus9.52e-169
nucleus of brain9.52e-169
basal ganglion1.45e-159
nuclear complex of neuraxis1.45e-159
aggregate regional part of brain1.45e-159
collection of basal ganglia1.45e-159
cerebral subcortex1.45e-159
anatomical cluster3.55e-15373
tube9.92e-14192
posterior neural tube2.36e-1315
chordal neural plate2.36e-1315
telencephalic nucleus2.46e-127
brainstem1.02e-116
diencephalon2.87e-117
future diencephalon2.87e-117
gyrus2.48e-106
segmental subdivision of nervous system3.38e-1013
organ part5.72e-10218
multi-tissue structure1.41e-09342
limbic system1.50e-095
anatomical conduit1.99e-09240
temporal lobe4.68e-096
parietal lobe6.35e-095
segmental subdivision of hindbrain7.67e-0912
hindbrain7.67e-0912
presumptive hindbrain7.67e-0912
occipital lobe9.41e-095
embryo8.08e-08592
corpus striatum1.03e-074
striatum1.03e-074
ventral part of telencephalon1.03e-074
future corpus striatum1.03e-074
regional part of diencephalon1.64e-074
multi-cellular organism2.40e-07656
spinal cord7.78e-073
dorsal region element7.78e-073
dorsum7.78e-073
pons9.49e-073


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
CTCF#1066444.288205098460020.005152015588243280.0239217248041853
RAD21#588548.284027116365060.0004011622639122450.00386503557940323
TAF1#687253.343046285745290.002394600090870310.0135132457389314



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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