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Coexpression cluster:C2319: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2319_Eosinophils_large_immature_Neutrophils_small_migratory_Mast
|full_id=C2319_Eosinophils_large_immature_Neutrophils_small_migratory_Mast
|id=C2319
|id=C2319

Revision as of 15:01, 12 September 2012


Full id: C2319_Eosinophils_large_immature_Neutrophils_small_migratory_Mast



Phase1 CAGE Peaks

Hg19::chr14:88459407..88459418,-p4@GALC
Hg19::chr14:88459424..88459442,-p5@GALC
Hg19::chr14:88459457..88459484,-p2@GALC
Hg19::chr14:88459487..88459500,-p3@GALC


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>

Uber Anatomy
Ontology termp-valuen
adult organism3.31e-26115
hematopoietic system4.01e-24102
blood island4.01e-24102
hemolymphoid system1.64e-21112
bone marrow1.53e-1880
bone element4.11e-1786
skeletal element2.42e-14101
skeletal system2.42e-14101
neural tube3.20e-1457
neural rod3.20e-1457
future spinal cord3.20e-1457
neural keel3.20e-1457
immune system4.48e-12115
anterior neural tube6.37e-1242
regional part of forebrain1.36e-1141
forebrain1.36e-1141
future forebrain1.36e-1141
regional part of brain1.85e-1159
gray matter6.37e-1034
brain grey matter6.37e-1034
telencephalon1.32e-0934
lateral plate mesoderm1.71e-09216
central nervous system1.87e-0982
regional part of telencephalon1.98e-0933
cerebral hemisphere1.02e-0832
brain5.02e-0869
future brain5.02e-0869
neural plate6.31e-0886
presumptive neural plate6.31e-0886
regional part of cerebral cortex1.55e-0722
musculoskeletal system1.83e-07167
regional part of nervous system4.88e-0794
nervous system4.88e-0794
neurectoderm6.13e-0790
neocortex9.49e-0720


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
ATF3#467422.46317452600873.92475754624726e-060.000127218421282594
BCL11A#53335428.36945510360711.542446414682e-065.8856982500173e-05
CTCF#1066445.360256373075030.001211145381643620.00816280411160805
E2F1#186944.907389214879320.001724022357361790.010637157853164
E2F6#187645.017155731697390.00157802193473060.00995993429874473
ELF1#199744.258097958807540.003041525565781240.016072348136239
GATA1#2623413.56030814380042.95627390049268e-050.000613573708055554
HEY1#2346244.040111043105710.00375304636917980.018576512310463
IRF1#365947.63716375356390.0002938853996185490.00307115241652608
IRF4#3662421.91451268674414.33289161192893e-060.000136220008145167
MAX#414946.452555509007120.0005767613195645490.00484955925078511
NFKB1#479045.488063424193840.001102199566301980.00767315161345236
PAX5#507946.669565531177830.0005052774169483260.00443450992845934
POU2F2#545249.106124057742520.000145395665174930.00188235749041831
SIN3A#2594245.408884726815140.001168172384885160.00795272509647486
SIX5#147912417.0867153554591.17257016123224e-050.000297310160400421
TAF1#687243.343046285745290.008005664898701650.0321702053234129
TBP#690843.706770687096390.005296377814784350.0243806594939291
TCF12#6938410.63446490218647.8163066689251e-050.00119924673453191
THAP1#55145431.36914460285131.03171810326891e-064.31351509156532e-05
USF1#739146.361499277207960.0006105011399140830.00507401946136296
USF2#7392412.99219738506963.50833029870167e-050.000680673431295009
YY1#752844.911170749853860.00171871838055440.0106699892377531
ZNF263#1012748.221841637010680.0002187871180958320.00248395562852599



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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