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Coexpression cluster:C2480: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000486!1.80e-21!82;UBERON:0000914!3.90e-21!83;UBERON:0002329!3.90e-21!83;UBERON:0003077!3.90e-21!83;UBERON:0003059!3.90e-21!83;UBERON:0007282!3.90e-21!83;UBERON:0009618!3.90e-21!83;UBERON:0007285!3.90e-21!83;UBERON:0004290!5.94e-21!70;UBERON:0005256!6.52e-21!143;UBERON:0001134!1.91e-19!61;UBERON:0002036!1.91e-19!61;UBERON:0003082!1.91e-19!61;UBERON:0002385!1.52e-18!63;UBERON:0001015!1.52e-18!63;UBERON:0000383!1.52e-18!63;UBERON:0002100!1.64e-18!216;UBERON:0003104!6.87e-18!238;UBERON:0009142!6.87e-18!238;UBERON:0000490!5.15e-15!138;UBERON:0003914!1.45e-14!118;UBERON:0000481!1.69e-13!347;UBERON:0002049!4.86e-13!79;UBERON:0007798!4.86e-13!79;UBERON:0004872!8.01e-13!84;UBERON:0000055!4.23e-12!69;UBERON:0000483!7.96e-12!309;UBERON:0001981!7.97e-12!60;UBERON:0007500!7.97e-12!60;UBERON:0004537!7.97e-12!60;UBERON:0006965!7.97e-12!60;UBERON:0000119!1.26e-11!312;UBERON:0000475!1.32e-11!365;UBERON:0003103!1.68e-10!69;UBERON:0001637!8.33e-10!42;UBERON:0003509!8.33e-10!42;UBERON:0004572!8.33e-10!42;UBERON:0001009!3.42e-09!113;UBERON:0004535!3.26e-08!110;UBERON:0007100!2.03e-07!27;UBERON:0004573!2.58e-07!33;UBERON:0004571!2.58e-07!33
|ontology_enrichment_uberon=UBERON:0000486!1.80e-21!82;UBERON:0000914!3.90e-21!83;UBERON:0002329!3.90e-21!83;UBERON:0003077!3.90e-21!83;UBERON:0003059!3.90e-21!83;UBERON:0007282!3.90e-21!83;UBERON:0009618!3.90e-21!83;UBERON:0007285!3.90e-21!83;UBERON:0004290!5.94e-21!70;UBERON:0005256!6.52e-21!143;UBERON:0001134!1.91e-19!61;UBERON:0002036!1.91e-19!61;UBERON:0003082!1.91e-19!61;UBERON:0002385!1.52e-18!63;UBERON:0001015!1.52e-18!63;UBERON:0000383!1.52e-18!63;UBERON:0002100!1.64e-18!216;UBERON:0003104!6.87e-18!238;UBERON:0009142!6.87e-18!238;UBERON:0000490!5.15e-15!138;UBERON:0003914!1.45e-14!118;UBERON:0000481!1.69e-13!347;UBERON:0002049!4.86e-13!79;UBERON:0007798!4.86e-13!79;UBERON:0004872!8.01e-13!84;UBERON:0000055!4.23e-12!69;UBERON:0000483!7.96e-12!309;UBERON:0001981!7.97e-12!60;UBERON:0007500!7.97e-12!60;UBERON:0004537!7.97e-12!60;UBERON:0006965!7.97e-12!60;UBERON:0000119!1.26e-11!312;UBERON:0000475!1.32e-11!365;UBERON:0003103!1.68e-10!69;UBERON:0001637!8.33e-10!42;UBERON:0003509!8.33e-10!42;UBERON:0004572!8.33e-10!42;UBERON:0001009!3.42e-09!113;UBERON:0004535!3.26e-08!110;UBERON:0007100!2.03e-07!27;UBERON:0004573!2.58e-07!33;UBERON:0004571!2.58e-07!33
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}}
}}

Revision as of 11:40, 5 September 2012


Full id: C2480_Mesenchymal_liposarcoma_skeletal_Alveolar_heart_left_Osteoblast



Phase1 CAGE Peaks

Hg19::chr19:1605424..1605474,-p1@UQCR11
Hg19::chr19:5680503..5680541,-p1@C19orf70
Hg19::chr19:5680543..5680554,-p2@C19orf70
Hg19::chr2:110970096..110970134,-p1@LINC00116


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
multilaminar epithelium1.80e-2182
somite3.90e-2183
paraxial mesoderm3.90e-2183
presomitic mesoderm3.90e-2183
presumptive segmental plate3.90e-2183
trunk paraxial mesoderm3.90e-2183
presumptive paraxial mesoderm3.90e-2183
dermomyotome5.94e-2170
trunk mesenchyme6.52e-21143
skeletal muscle tissue1.91e-1961
striated muscle tissue1.91e-1961
myotome1.91e-1961
muscle tissue1.52e-1863
musculature1.52e-1863
musculature of body1.52e-1863
trunk1.64e-18216
mesenchyme6.87e-18238
entire embryonic mesenchyme6.87e-18238
unilaminar epithelium5.15e-15138
epithelial tube1.45e-14118
multi-tissue structure1.69e-13347
vasculature4.86e-1379
vascular system4.86e-1379
splanchnic layer of lateral plate mesoderm8.01e-1384
vessel4.23e-1269
epithelium7.96e-12309
blood vessel7.97e-1260
epithelial tube open at both ends7.97e-1260
blood vasculature7.97e-1260
vascular cord7.97e-1260
cell layer1.26e-11312
organism subdivision1.32e-11365
compound organ1.68e-1069
artery8.33e-1042
arterial blood vessel8.33e-1042
arterial system8.33e-1042
circulatory system3.42e-09113
cardiovascular system3.26e-08110
primary circulatory organ2.03e-0727
systemic artery2.58e-0733
systemic arterial system2.58e-0733


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
BCLAF1#9774210.82632380506090.01202203816432580.043653766909256
CCNT2#90534.752151182721970.01386206996689490.048722512124673
ELF1#199744.258097958807540.003041525565781240.0160894437808148
ESR1#2099215.38430164807720.006065572629693510.026839060283547
ETS1#211337.296570691651750.00400857377511390.019205075301579
FOXA1#316938.311064812039090.002740138182109850.0150366378521107
FOXA2#3170318.47284781449890.0002594484187437260.00278198494919671
GABPB1#255335.300762877136630.01012678824234270.0378590935438872
HEY1#2346244.040111043105710.00375304636917980.0186056111335629
MAX#414946.452555509007120.0005767613195645490.00485424896881311
MXI1#460137.471178721569470.003741314738550960.0186350233679666
MYC#460945.22228187160940.001344309395272740.00887754213929114
NANOG#79923214.62238924050630.006698757715363760.0284892925452977
NR2C2#7182324.46095817893070.0001125906063438030.00155581507487966
NRF1#489939.157709585783180.002061953791733420.0119618059242819
PAX5#507946.669565531177830.0005052774169483260.00443823954151944
SETDB1#9869220.16001308900520.00356908685407640.0180859709826728
SIN3A#2594245.408884726815140.001168172384885160.00796362635150267
SREBF1#6720223.50292472024410.002638454900768240.0145836248415631
SRF#6722413.79717826216782.75840773062708e-050.000584470166319661
TAF1#687243.343046285745290.008005664898701650.0322235185707597
TBP#690843.706770687096390.005296377814784350.0244226412909295
TCF7L2#693438.077632422353010.002978381685834620.0158638925380907
ZBTB7A#5134135.513931980906920.009038352821081090.0342435075919933



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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