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Coexpression cluster:C2143: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0017060!3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity!0.0082879592865696!2527$GO:0046920!alpha(1,3)-fucosyltransferase activity!0.0082879592865696!2527$GO:0019317!fucose catabolic process!0.0082879592865696!2527$GO:0042355!L-fucose catabolic process!0.0082879592865696!2527$GO:0042354!L-fucose metabolic process!0.0082879592865696!2527$GO:0006004!fucose metabolic process!0.00941758099038374!2527$GO:0008417!fucosyltransferase activity!0.00968622692758105!2527$GO:0019320!hexose catabolic process!0.0480923729825549!2527$GO:0046365!monosaccharide catabolic process!0.0480923729825549!2527$GO:0046164!alcohol catabolic process!0.0480923729825549!2527$GO:0006486!protein amino acid glycosylation!0.0480923729825549!2527$GO:0043413!biopolymer glycosylation!0.0480923729825549!2527$GO:0009101!glycoprotein biosynthetic process!0.0480923729825549!2527$GO:0044275!cellular carbohydrate catabolic process!0.0480923729825549!2527$GO:0016052!carbohydrate catabolic process!0.0480923729825549!2527$GO:0009100!glycoprotein metabolic process!0.0488322814096535!2527
|gostat_on_coexpression_clusters=GO:0017060!3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity!0.0082879592865696!2527$GO:0046920!alpha(1,3)-fucosyltransferase activity!0.0082879592865696!2527$GO:0019317!fucose catabolic process!0.0082879592865696!2527$GO:0042355!L-fucose catabolic process!0.0082879592865696!2527$GO:0042354!L-fucose metabolic process!0.0082879592865696!2527$GO:0006004!fucose metabolic process!0.00941758099038374!2527$GO:0008417!fucosyltransferase activity!0.00968622692758105!2527$GO:0019320!hexose catabolic process!0.0480923729825549!2527$GO:0046365!monosaccharide catabolic process!0.0480923729825549!2527$GO:0046164!alcohol catabolic process!0.0480923729825549!2527$GO:0006486!protein amino acid glycosylation!0.0480923729825549!2527$GO:0043413!biopolymer glycosylation!0.0480923729825549!2527$GO:0009101!glycoprotein biosynthetic process!0.0480923729825549!2527$GO:0044275!cellular carbohydrate catabolic process!0.0480923729825549!2527$GO:0016052!carbohydrate catabolic process!0.0480923729825549!2527$GO:0009100!glycoprotein metabolic process!0.0488322814096535!2527
|id=C2143
|id=C2143
|ontology_enrichment_celltype=CL:0000183!4.37e-17!59;CL:0000222!1.10e-16!119;CL:0002321!1.80e-16!248;CL:0000220!3.08e-16!246;CL:0000393!8.50e-15!60;CL:0000211!8.50e-15!60;CL:0000187!2.38e-14!54;CL:0000680!1.26e-13!57;CL:0000056!1.26e-13!57;CL:0000355!1.26e-13!57;CL:0000055!2.18e-13!180;CL:0000192!3.55e-12!42;CL:0000514!3.55e-12!42;CL:0000012!5.20e-10!682;CL:0000548!1.07e-09!679;CL:0000004!1.07e-09!679;CL:0000255!1.07e-09!679;CL:0000359!3.94e-09!32;CL:0000144!5.53e-09!625;CL:0002371!1.84e-08!591;CL:0000066!6.68e-08!254;CL:1000449!3.90e-07!16
|ontology_enrichment_celltype=CL:0000222!3.77e-17!121;CL:0000183!1.26e-16!59;CL:0002321!1.86e-16!250;CL:0000393!5.52e-15!61;CL:0000211!5.52e-15!61;CL:0000187!2.19e-14!55;CL:0000680!1.30e-13!58;CL:0000056!1.30e-13!58;CL:0000355!1.30e-13!58;CL:0000192!9.45e-13!43;CL:0000514!9.45e-13!43;CL:0000055!1.54e-12!106;CL:0000359!2.05e-09!32;CL:0000548!4.64e-09!679;CL:0000255!4.64e-09!679;CL:0002371!1.26e-07!588;CL:0000066!1.76e-07!253
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004290!3.08e-16!70;UBERON:0005256!4.14e-16!143;UBERON:0000914!2.24e-15!83;UBERON:0002329!2.24e-15!83;UBERON:0003077!2.24e-15!83;UBERON:0003059!2.24e-15!83;UBERON:0007282!2.24e-15!83;UBERON:0009618!2.24e-15!83;UBERON:0007285!2.24e-15!83;UBERON:0000486!2.44e-15!82;UBERON:0001134!8.79e-14!61;UBERON:0002036!8.79e-14!61;UBERON:0003082!8.79e-14!61;UBERON:0002385!7.17e-13!63;UBERON:0001015!7.17e-13!63;UBERON:0000383!7.17e-13!63;UBERON:0003104!8.77e-12!238;UBERON:0009142!8.77e-12!238;UBERON:0002100!1.12e-11!216;UBERON:0003914!1.35e-11!118;UBERON:0000490!6.25e-11!138;UBERON:0002049!2.48e-09!79;UBERON:0007798!2.48e-09!79;UBERON:0000055!6.97e-08!69;UBERON:0004872!8.83e-08!84;UBERON:0001981!2.92e-07!60;UBERON:0007500!2.92e-07!60;UBERON:0004537!2.92e-07!60;UBERON:0006965!2.92e-07!60;UBERON:0001637!2.98e-07!42;UBERON:0003509!2.98e-07!42;UBERON:0004572!2.98e-07!42;UBERON:0004211!3.90e-07!16;UBERON:0001285!3.90e-07!16;UBERON:0007684!3.90e-07!16;UBERON:0003220!3.90e-07!16;UBERON:0004208!3.90e-07!16;UBERON:0000080!3.97e-07!18;UBERON:0002120!3.97e-07!18;UBERON:0004875!3.97e-07!18;UBERON:0005721!3.97e-07!18;UBERON:0005754!3.97e-07!18;UBERON:0007297!3.97e-07!18;UBERON:0006555!5.42e-07!17;UBERON:0005103!5.42e-07!17;UBERON:0000083!5.42e-07!17;UBERON:0009201!5.42e-07!17;UBERON:0004819!5.42e-07!17;UBERON:0006553!5.42e-07!17;UBERON:0003074!5.42e-07!17;UBERON:0003060!5.42e-07!17
|ontology_enrichment_uberon=UBERON:0007503!1.13e-19!78;UBERON:0002329!2.19e-16!71;UBERON:0003059!2.19e-16!71;UBERON:0007282!2.19e-16!71;UBERON:0004290!2.19e-16!71;UBERON:0009618!2.19e-16!71;UBERON:0007524!2.40e-16!73;UBERON:0003077!6.58e-16!72;UBERON:0007285!6.58e-16!72;UBERON:0000486!1.04e-15!83;UBERON:0001134!3.65e-14!62;UBERON:0002036!3.65e-14!62;UBERON:0003082!3.65e-14!62;UBERON:0003104!3.92e-14!160;UBERON:0009142!3.92e-14!160;UBERON:0005256!1.81e-13!122;UBERON:0002385!3.42e-13!64;UBERON:0001015!3.42e-13!64;UBERON:0000383!3.42e-13!64;UBERON:0000490!6.26e-13!148;UBERON:0003914!9.47e-11!117;UBERON:0002100!9.58e-11!199;UBERON:0000475!1.87e-10!264;UBERON:0002049!1.99e-09!78;UBERON:0007798!1.99e-09!78;UBERON:0004872!3.61e-08!83;UBERON:0000055!5.29e-08!68;UBERON:0001637!1.59e-07!42;UBERON:0003509!1.59e-07!42;UBERON:0004572!1.59e-07!42;UBERON:0007500!2.07e-07!59;UBERON:0001981!2.07e-07!59;UBERON:0004537!2.07e-07!59;UBERON:0006965!2.07e-07!59;UBERON:0000119!9.09e-07!309;UBERON:0000483!9.19e-07!306
|tf_chipseq_enrich=ATF3#467;2:11.2315872630044:0.0111955903992222:0.0411188727565187!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0172888301231706!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106258584231636!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160544773357236!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0191962692695273!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.01855540663467!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186208144290661!NANOG#79923;2:14.6223892405063:0.00669875771536376:0.0284800145342917!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.00079190722762911!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434705284869787!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188072552330994!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00794340488996815!SREBF1#6720;2:23.5029247202441:0.00263845490076824:0.0145805381968006!SRF#6722;3:10.3478836966259:0.00143989377840126:0.0092354643691242!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321257064610582!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.00096743572915325!TBP#6908;4:3.70677068709639:0.00529637781478435:0.024349535704462!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482732164559964!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106611171198385!ZBTB33#10009;2:15.8323625149906:0.00573424893032464:0.025833803124587
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}}
}}

Revision as of 12:07, 19 October 2012


Full id: C2143_Mesenchymal_Alveolar_Osteoblast_Renal_Adipocyte_Placental_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:61560053..61560091,-p1@C11orf10
Hg19::chr17:7307407..7307424,-p1@C17orf61
p1@PLSCR3
Hg19::chr19:5903739..5903809,-p1@FUT5
p1@NDUFA11
Hg19::chr2:113342163..113342210,+p1@CHCHD5


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


GO IDGO nameFDR corrected p-value
GO:00170603-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity0.0082879592865696
GO:0046920alpha(1,3)-fucosyltransferase activity0.0082879592865696
GO:0019317fucose catabolic process0.0082879592865696
GO:0042355L-fucose catabolic process0.0082879592865696
GO:0042354L-fucose metabolic process0.0082879592865696
GO:0006004fucose metabolic process0.00941758099038374
GO:0008417fucosyltransferase activity0.00968622692758105
GO:0019320hexose catabolic process0.0480923729825549
GO:0046365monosaccharide catabolic process0.0480923729825549
GO:0046164alcohol catabolic process0.0480923729825549
GO:0006486protein amino acid glycosylation0.0480923729825549
GO:0043413biopolymer glycosylation0.0480923729825549
GO:0009101glycoprotein biosynthetic process0.0480923729825549
GO:0044275cellular carbohydrate catabolic process0.0480923729825549
GO:0016052carbohydrate catabolic process0.0480923729825549
GO:0009100glycoprotein metabolic process0.0488322814096535



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
epithelial vesicle1.13e-1978
somite2.19e-1671
presomitic mesoderm2.19e-1671
presumptive segmental plate2.19e-1671
dermomyotome2.19e-1671
trunk paraxial mesoderm2.19e-1671
dense mesenchyme tissue2.40e-1673
paraxial mesoderm6.58e-1672
presumptive paraxial mesoderm6.58e-1672
multilaminar epithelium1.04e-1583
skeletal muscle tissue3.65e-1462
striated muscle tissue3.65e-1462
myotome3.65e-1462
mesenchyme3.92e-14160
entire embryonic mesenchyme3.92e-14160
trunk mesenchyme1.81e-13122
muscle tissue3.42e-1364
musculature3.42e-1364
musculature of body3.42e-1364
unilaminar epithelium6.26e-13148
epithelial tube9.47e-11117
trunk9.58e-11199
organism subdivision1.87e-10264
vasculature1.99e-0978
vascular system1.99e-0978
splanchnic layer of lateral plate mesoderm3.61e-0883
vessel5.29e-0868
artery1.59e-0742
arterial blood vessel1.59e-0742
arterial system1.59e-0742
epithelial tube open at both ends2.07e-0759
blood vessel2.07e-0759
blood vasculature2.07e-0759
vascular cord2.07e-0759
cell layer9.09e-07309
epithelium9.19e-07306


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#467211.23158726300440.01119559039922220.0411188727565187
CHD2#110637.758017125587640.003351522464536340.0172888301231706
E2F1#186944.907389214879320.001724022357361790.0106258584231636
ELF1#199744.258097958807540.003041525565781240.0160544773357236
ETS1#211337.296570691651750.00400857377511390.0191962692695273
HEY1#2346244.040111043105710.00375304636917980.01855540663467
MXI1#460137.471178721569470.003741314738550960.0186208144290661
NANOG#79923214.62238924050630.006698757715363760.0284800145342917
NRF1#4899412.21027944771094.49717228915276e-050.00079190722762911
PAX5#507935.002174148383370.01196533174786410.0434705284869787
POU2F2#545249.106124057742520.000145395665174930.00188072552330994
SIN3A#2594245.408884726815140.001168172384885160.00794340488996815
SREBF1#6720223.50292472024410.002638454900768240.0145805381968006
SRF#6722310.34788369662590.001439893778401260.0092354643691242
TAF1#687243.343046285745290.008005664898701650.0321257064610582
TAF7#6879411.43306940492395.85061525419808e-050.00096743572915325
TBP#690843.706770687096390.005296377814784350.024349535704462
USF1#739134.771124457905970.01370465887188020.0482732164559964
YY1#752844.911170749853860.00171871838055440.0106611171198385
ZBTB33#10009215.83236251499060.005734248930324640.025833803124587



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.