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Coexpression cluster:C2272: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2272_amniotic_chorionic_oral_glassy_colon_epidermoid_Mallassezderived
|full_id=C2272_amniotic_chorionic_oral_glassy_colon_epidermoid_Mallassezderived
|id=C2272
|id=C2272

Revision as of 14:58, 12 September 2012


Full id: C2272_amniotic_chorionic_oral_glassy_colon_epidermoid_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr13:80055378..80055401,+p5@NDFIP2
Hg19::chr13:80055403..80055426,+p1@NDFIP2
Hg19::chr13:80055432..80055449,+p4@NDFIP2
Hg19::chr13:80055462..80055478,+p6@NDFIP2


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>disease_data<br>

Cell Type
Ontology termp-valuen
endo-epithelial cell5.04e-1443
endodermal cell8.20e-1359
epithelial cell of alimentary canal5.06e-1121
epithelial cell1.25e-10254
Uber Anatomy
Ontology termp-valuen
multi-tissue structure3.66e-20347
organism subdivision5.91e-20365
organ part3.54e-17219
endoderm-derived structure2.29e-16169
endoderm2.29e-16169
presumptive endoderm2.29e-16169
organ4.26e-16511
ectoderm-derived structure7.74e-16169
ectoderm4.25e-15173
presumptive ectoderm4.25e-15173
digestive system1.40e-13155
digestive tract1.40e-13155
primitive gut1.40e-13155
regional part of forebrain9.06e-1341
forebrain9.06e-1341
future forebrain9.06e-1341
telencephalon2.77e-1234
head3.00e-12123
anterior neural tube4.97e-1242
subdivision of digestive tract5.54e-12129
endodermal part of digestive tract5.54e-12129
anatomical system7.81e-12625
cerebral hemisphere8.44e-1232
anterior region of body8.68e-12129
craniocervical region8.68e-12129
anatomical group1.05e-11626
regional part of telencephalon1.09e-1133
gray matter1.51e-1134
brain grey matter1.51e-1134
neural tube1.67e-1157
neural rod1.67e-1157
future spinal cord1.67e-1157
neural keel1.67e-1157
multi-cellular organism1.73e-11659
regional part of brain3.18e-1159
regional part of cerebral cortex2.87e-1022
brain4.64e-1069
future brain4.64e-1069
epithelium8.01e-10309
mixed endoderm/mesoderm-derived structure1.04e-09130
central nervous system1.21e-0982
neocortex2.21e-0920
cell layer2.27e-09312
regional part of nervous system3.11e-0994
nervous system3.11e-0994
embryonic structure6.48e-09605
developing anatomical structure6.48e-09605
germ layer8.05e-09604
embryonic tissue8.05e-09604
presumptive structure8.05e-09604
epiblast (generic)8.05e-09604
cerebral cortex8.76e-0925
pallium8.76e-0925
organ component layer1.71e-0857
mesenchyme1.76e-08238
entire embryonic mesenchyme1.76e-08238
adult organism1.81e-08115
embryo2.32e-08612
anatomical cluster3.50e-08286
neural plate5.85e-0886
presumptive neural plate5.85e-0886
pre-chordal neural plate5.88e-0861
surface structure1.17e-0795
neurectoderm2.81e-0790
anatomical conduit4.45e-07241
mucosa4.80e-0712
intestine7.15e-0727
extraembryonic membrane8.69e-0714
membranous layer8.69e-0714
gastrointestinal system9.98e-0735
Disease
Ontology termp-valuen
cell type cancer1.14e-08143
carcinoma2.11e-08106
female reproductive organ cancer7.31e-0727


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#90546.336201576962630.0006203100587215640.0051156476802607
E2F1#186944.907389214879320.001724022357361790.010633388707288
E2F6#187645.017155731697390.00157802193473060.00995632410084752
EGR1#195844.988179094810140.001615011500076050.0101321671205889
ELF1#199744.258097958807540.003041525565781240.0160674703371081
ELK4#2005416.2356816584681.43847748454449e-050.000343076387322087
ETS1#211349.728760922202340.0001115955317418140.00154369877345474
GABPB1#255347.067683836182170.0004006876864423170.00389931245661099
HEY1#2346244.040111043105710.00375304636917980.0185694717524526
HMGN3#932448.178547723350590.0002234570284440470.002477981375416
IRF1#365947.63716375356390.0002938853996185490.00307053794025226
MYC#460945.22228187160940.001344309395272740.00886353086697534
NFKB1#479045.488063424193840.001102199566301980.00767161749450265
NRF1#4899412.21027944771094.49717228915276e-050.00079257539100038
PAX5#507946.669565531177830.0005052774169483260.00443376475791179
POU2F2#545249.106124057742520.000145395665174930.00188212417888008
SIN3A#2594245.408884726815140.001168172384885160.00795013395705857
SPI1#668848.204323508522730.000220661881527680.00249304481229656
TAF1#687243.343046285745290.008005664898701650.0321565953753895
TBP#690843.706770687096390.005296377814784350.0243720656766947
ZEB1#6935416.88843201754391.22862303393937e-050.000303635023761462
ZNF263#1012748.221841637010680.0002187871180958320.00248233653740474



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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