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Coexpression cluster:C2783: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2783_medulla_optic_blood_Whole_Hepatocyte_substantia_corpus
|full_id=C2783_medulla_optic_blood_Whole_Hepatocyte_substantia_corpus
|id=C2783
|id=C2783

Revision as of 15:33, 12 September 2012


Full id: C2783_medulla_optic_blood_Whole_Hepatocyte_substantia_corpus



Phase1 CAGE Peaks

Hg19::chr4:170947459..170947472,-p4@MFAP3L
Hg19::chr4:170947485..170947499,-p2@MFAP3L
Hg19::chr4:170947522..170947563,-p1@MFAP3L
Hg19::chr4:170947565..170947583,-p3@MFAP3L


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.14e-39115
regional part of nervous system1.93e-2994
nervous system1.93e-2994
neural tube9.56e-2957
neural rod9.56e-2957
future spinal cord9.56e-2957
neural keel9.56e-2957
central nervous system6.23e-2882
regional part of brain1.33e-2359
brain2.01e-2369
future brain2.01e-2369
anterior neural tube1.12e-2242
regional part of forebrain1.91e-2241
forebrain1.91e-2241
future forebrain1.91e-2241
neural plate4.31e-2286
presumptive neural plate4.31e-2286
neurectoderm6.90e-2190
telencephalon7.38e-1934
gray matter8.47e-1934
brain grey matter8.47e-1934
regional part of telencephalon3.11e-1833
cerebral hemisphere1.71e-1732
pre-chordal neural plate4.72e-1761
ectoderm-derived structure1.39e-16169
ectoderm4.66e-16173
presumptive ectoderm4.66e-16173
head4.81e-15123
anterior region of body6.11e-14129
craniocervical region6.11e-14129
cerebral cortex2.23e-1325
pallium2.23e-1325
regional part of cerebral cortex2.42e-1222
organism subdivision2.37e-11365
neocortex3.11e-1120
tube5.30e-10194
anatomical conduit1.10e-08241
multi-cellular organism3.04e-08659
posterior neural tube2.84e-0715
chordal neural plate2.84e-0715
nucleus of brain5.85e-079
neural nucleus5.85e-079
basal ganglion8.62e-079
nuclear complex of neuraxis8.62e-079
aggregate regional part of brain8.62e-079
collection of basal ganglia8.62e-079
cerebral subcortex8.62e-079


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
CCNT2#90546.336201576962630.0006203100587215640.00513185695681412
CTCF#1066445.360256373075030.001211145381643620.00819134908130283
E2F1#186944.907389214879320.001724022357361790.0106718332729082
E2F6#187645.017155731697390.00157802193473060.00998588420027442
EGR1#195844.988179094810140.001615011500076050.0101602425189111
ELF1#199744.258097958807540.003041525565781240.0161188353663483
HEY1#2346244.040111043105710.00375304636917980.0186472126427578
IRF1#365947.63716375356390.0002938853996185490.00307978098040956
JUND#372746.994663941871030.000417684217818580.00392253592525444
NRF1#4899412.21027944771094.49717228915276e-050.000794990143376481
PAX5#507946.669565531177830.0005052774169483260.00444646681400962
RAD21#5885410.35503389545638.6948481184721e-050.00129781512454639
SP1#666745.69838137814090.0009482606065333980.00685366017202364
TAF1#687243.343046285745290.008005664898701650.0323019485533728
TCF7L2#6934410.77017656313737.42969445082454e-050.00115658050193719
YY1#752844.911170749853860.00171871838055440.010700520354499



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.