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Coexpression cluster:C2764: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!4.12e-08!14;DOID:120!3.51e-07!27;DOID:193!6.16e-07!29
|ontology_enrichment_disease=DOID:2394!4.12e-08!14;DOID:120!3.51e-07!27;DOID:193!6.16e-07!29
|ontology_enrichment_uberon=UBERON:0005256!1.04e-24!143;UBERON:0000119!2.58e-23!312;UBERON:0000475!7.95e-23!365;UBERON:0000483!1.13e-22!309;UBERON:0003914!6.91e-21!118;UBERON:0000486!1.43e-20!82;UBERON:0002100!7.30e-20!216;UBERON:0000914!3.74e-19!83;UBERON:0002329!3.74e-19!83;UBERON:0003077!3.74e-19!83;UBERON:0003059!3.74e-19!83;UBERON:0007282!3.74e-19!83;UBERON:0009618!3.74e-19!83;UBERON:0007285!3.74e-19!83;UBERON:0004290!1.81e-18!70;UBERON:0000490!1.99e-18!138;UBERON:0000481!1.79e-17!347;UBERON:0001134!5.76e-17!61;UBERON:0002036!5.76e-17!61;UBERON:0003082!5.76e-17!61;UBERON:0003104!1.25e-16!238;UBERON:0009142!1.25e-16!238;UBERON:0002049!1.84e-16!79;UBERON:0007798!1.84e-16!79;UBERON:0002385!4.40e-16!63;UBERON:0001015!4.40e-16!63;UBERON:0000383!4.40e-16!63;UBERON:0001637!1.84e-15!42;UBERON:0003509!1.84e-15!42;UBERON:0004572!1.84e-15!42;UBERON:0000468!5.22e-15!659;UBERON:0000467!7.95e-14!625;UBERON:0000480!1.45e-13!626;UBERON:0004872!3.37e-13!84;UBERON:0001981!3.96e-13!60;UBERON:0007500!3.96e-13!60;UBERON:0004537!3.96e-13!60;UBERON:0006965!3.96e-13!60;UBERON:0000055!6.27e-13!69;UBERON:0004573!1.08e-12!33;UBERON:0004571!1.08e-12!33;UBERON:0000477!3.75e-11!286;UBERON:0001048!6.79e-11!168;UBERON:0004111!1.52e-10!241;UBERON:0002050!1.67e-10!605;UBERON:0005423!1.67e-10!605;UBERON:0004535!1.69e-10!110;UBERON:0000923!1.75e-10!604;UBERON:0005291!1.75e-10!604;UBERON:0006598!1.75e-10!604;UBERON:0002532!1.75e-10!604;UBERON:0000922!1.99e-10!612;UBERON:0001009!3.58e-10!113;UBERON:0003102!6.12e-09!95;UBERON:0000025!2.06e-08!194;UBERON:0007625!1.09e-07!11;UBERON:0000466!1.20e-07!126;UBERON:0002199!1.66e-07!45;UBERON:0002416!1.66e-07!45;UBERON:0003886!3.30e-07!63;UBERON:0005085!4.40e-07!29;UBERON:0000464!6.32e-07!104
|ontology_enrichment_uberon=UBERON:0005256!1.04e-24!143;UBERON:0000119!2.58e-23!312;UBERON:0000475!7.95e-23!365;UBERON:0000483!1.13e-22!309;UBERON:0003914!6.91e-21!118;UBERON:0000486!1.43e-20!82;UBERON:0002100!7.30e-20!216;UBERON:0000914!3.74e-19!83;UBERON:0002329!3.74e-19!83;UBERON:0003077!3.74e-19!83;UBERON:0003059!3.74e-19!83;UBERON:0007282!3.74e-19!83;UBERON:0009618!3.74e-19!83;UBERON:0007285!3.74e-19!83;UBERON:0004290!1.81e-18!70;UBERON:0000490!1.99e-18!138;UBERON:0000481!1.79e-17!347;UBERON:0001134!5.76e-17!61;UBERON:0002036!5.76e-17!61;UBERON:0003082!5.76e-17!61;UBERON:0003104!1.25e-16!238;UBERON:0009142!1.25e-16!238;UBERON:0002049!1.84e-16!79;UBERON:0007798!1.84e-16!79;UBERON:0002385!4.40e-16!63;UBERON:0001015!4.40e-16!63;UBERON:0000383!4.40e-16!63;UBERON:0001637!1.84e-15!42;UBERON:0003509!1.84e-15!42;UBERON:0004572!1.84e-15!42;UBERON:0000468!5.22e-15!659;UBERON:0000467!7.95e-14!625;UBERON:0000480!1.45e-13!626;UBERON:0004872!3.37e-13!84;UBERON:0001981!3.96e-13!60;UBERON:0007500!3.96e-13!60;UBERON:0004537!3.96e-13!60;UBERON:0006965!3.96e-13!60;UBERON:0000055!6.27e-13!69;UBERON:0004573!1.08e-12!33;UBERON:0004571!1.08e-12!33;UBERON:0000477!3.75e-11!286;UBERON:0001048!6.79e-11!168;UBERON:0004111!1.52e-10!241;UBERON:0002050!1.67e-10!605;UBERON:0005423!1.67e-10!605;UBERON:0004535!1.69e-10!110;UBERON:0000923!1.75e-10!604;UBERON:0005291!1.75e-10!604;UBERON:0006598!1.75e-10!604;UBERON:0002532!1.75e-10!604;UBERON:0000922!1.99e-10!612;UBERON:0001009!3.58e-10!113;UBERON:0003102!6.12e-09!95;UBERON:0000025!2.06e-08!194;UBERON:0007625!1.09e-07!11;UBERON:0000466!1.20e-07!126;UBERON:0002199!1.66e-07!45;UBERON:0002416!1.66e-07!45;UBERON:0003886!3.30e-07!63;UBERON:0005085!4.40e-07!29;UBERON:0000464!6.32e-07!104
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}}
}}

Revision as of 14:19, 5 September 2012


Full id: C2764_Smooth_Lens_Renal_Ciliary_Mesothelial_mucinous_glioblastoma



Phase1 CAGE Peaks

Hg19::chr3:98620486..98620493,-p4@DCBLD2
Hg19::chr3:98620500..98620547,-p1@DCBLD2
Hg19::chr3:98620631..98620663,-p13@DCBLD2
Hg19::chr3:98620849..98620854,-p32@DCBLD2


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>

Uber Anatomy
Ontology termp-valuen
trunk mesenchyme1.04e-24143
cell layer2.58e-23312
organism subdivision7.95e-23365
epithelium1.13e-22309
epithelial tube6.91e-21118
multilaminar epithelium1.43e-2082
trunk7.30e-20216
somite3.74e-1983
paraxial mesoderm3.74e-1983
presomitic mesoderm3.74e-1983
presumptive segmental plate3.74e-1983
trunk paraxial mesoderm3.74e-1983
presumptive paraxial mesoderm3.74e-1983
dermomyotome1.81e-1870
unilaminar epithelium1.99e-18138
multi-tissue structure1.79e-17347
skeletal muscle tissue5.76e-1761
striated muscle tissue5.76e-1761
myotome5.76e-1761
mesenchyme1.25e-16238
entire embryonic mesenchyme1.25e-16238
vasculature1.84e-1679
vascular system1.84e-1679
muscle tissue4.40e-1663
musculature4.40e-1663
musculature of body4.40e-1663
artery1.84e-1542
arterial blood vessel1.84e-1542
arterial system1.84e-1542
multi-cellular organism5.22e-15659
anatomical system7.95e-14625
anatomical group1.45e-13626
splanchnic layer of lateral plate mesoderm3.37e-1384
blood vessel3.96e-1360
epithelial tube open at both ends3.96e-1360
blood vasculature3.96e-1360
vascular cord3.96e-1360
vessel6.27e-1369
systemic artery1.08e-1233
systemic arterial system1.08e-1233
anatomical cluster3.75e-11286
primordium6.79e-11168
anatomical conduit1.52e-10241
embryonic structure1.67e-10605
developing anatomical structure1.67e-10605
cardiovascular system1.69e-10110
germ layer1.75e-10604
embryonic tissue1.75e-10604
presumptive structure1.75e-10604
epiblast (generic)1.75e-10604
embryo1.99e-10612
circulatory system3.58e-10113
surface structure6.12e-0995
tube2.06e-08194
pigment epithelium of eye1.09e-0711
immaterial anatomical entity1.20e-07126
integument1.66e-0745
integumental system1.66e-0745
body cavity precursor3.30e-0763
ectodermal placode4.40e-0729
anatomical space6.32e-07104
Disease
Ontology termp-valuen
ovarian cancer4.12e-0814
female reproductive organ cancer3.51e-0727
reproductive organ cancer6.16e-0729


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#90546.336201576962630.0006203100587215640.00513145047309477
CHD2#1106410.34402283411698.73193255208051e-050.00129245224462406
E2F1#186944.907389214879320.001724022357361790.0106686716229489
E2F6#187645.017155731697390.00157802193473060.0099846742300575
EGR1#195844.988179094810140.001615011500076050.0101590186144939
ELF1#199744.258097958807540.003041525565781240.0161171996836281
EP300#203346.77394172622320.0004748459821442640.00434868813829926
FOS#235348.99795530889440.0001525147711168630.00195202085547476
HEY1#2346244.040111043105710.00375304636917980.0186445516696366
IRF1#365935.727872815172930.008097114790333330.0320166043837361
MYC#460945.22228187160940.001344309395272740.0088893458865955
NFYA#4800418.42558069983058.67100748407158e-060.000234974403380631
NFYB#4801312.56984494015230.000811456397697350.00619229100680356
PAX5#507935.002174148383370.01196533174786410.043515941164299
POU2F2#545249.106124057742520.000145395665174930.00188586411763592
RFX5#5993412.04791082719514.74457429336527e-050.000827795848020006
SP1#666745.69838137814090.0009482606065333980.006853185903103
SP2#6668426.15353049384462.13562021071447e-067.75798397171509e-05
TAF1#687243.343046285745290.008005664898701650.0322957100063927
TAF7#687938.574802053692940.00250055433515240.0140375937545141
TBP#690843.706770687096390.005296377814784350.024478842439185
ZNF263#1012748.221841637010680.0002187871180958320.00249589380959154



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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