Personal tools

Coexpression cluster:C4726: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0.0954252957357428,0.490436573121534,0,0.101667003219354,0,0,0.223320720221072,0.204850754147253,0,0,0.0504265701716883,0.148603081231402,0,0.196582913874522,0.149411045406522,0.0972869140252862,0,0,0,0,0,0,0.453141290572041,0,0.324130534851672,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0522561809686404,0,0,0,0,0,0.0392295810357272,0,0.0365629421359175,0,0.134908379262287,0,0,0,0,0,0,0,0,0,0.12941289334046,0,0,0.375771526791093,0.211383522176996,0.180937916953831,0,0,0.256635648918622,0,0.0948420448069823,0.135979123430744,0.257712632750166,0.132643503184185,0.087969206950705,0.126402372315621,0,0,0.073058801099379,0,0,0.157182883491893,0,0.0517815087208527,0.14526713795306,0,0,0,0,0,0,0.0548851394659095,0.173298677647464,0,0,0,0.117986819981215,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.127200899524475,0,0,0,0,0.0425961947748989,0,0,0.0677314085379025,0,0,0,0,0,0,0,0.141926672950355,0.104741781954859,0.109512603169101,0,0,0,0,0,0,0,0,0,0.165650208579294,0.23600275090536,0.0922340184907578,0.177754045794409,0.236293617851166,0.248477885595747,0.320021012625357,0.168656922891142,0.288655857957696,0.0778115911724362,0,0,0,0,0,0,0,0,0,0.0955099827348378,0.128119866952565,0.123606948733483,0.327158097282158,0.231393838911783,0.324500852948893,0,0,0,0,0,0.110162914233654,0,0,0,0,0,0,0,0,0.223217704226089,0.153913991558631,0.335309592416312,0.272283065509648,0.332468362080336,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0863651195885523,0,0,0,0,0,0,0,0.102578507776567,0,0,0,0,0.132064901528981,0,0.114423942847335,0,0,0,0,0,0.170041493096301,0,0,0.110442433690542,0.0811586845710415,0,0,0,0,0,0,0,0,0,0.214297657915009,0,0,0,0,0,0.10423609841563,0,0,0,0,0.114259303421121,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0962521000248044,0,0,0,0,0,0,0,0,0,0.181630511148827,0.129893181862632,0.0495511575604446,0.146442146711949,0.341840505197881,0,0,0,0.161727153872444,0.141473819015711,0,0,0,0,0.127165533945345,0.0849035433286077,0,0,0,0.178905770687666,0.262706372468367,0.160693426449034,0,0,0.179810294710844,0.123202864573785,0,0,0,0,0,0,0,0,0.0622241049201175,0.164504839448406,0.105739413005624,0,0.198675441186397,0.068354073672271,0.0370406554214911,0.174889423717366,0.197713313938225,0.332138271320857,0.0800184682686384,0.165791835868262,0,0,0,0.185345510730693,0,0.136926075558615,0.109325311288728,0.137404238899705,0,0,0.0989542966657617,0,0,0.251625724314337,0,0,0,0.079970395058755,0.620157552899625,0.152673061679609,0,0.238332309002125,0,0,0,0,0,0,0,0.198320387665648,0,0.147929950453612,0,0,0,0,0,0,0,0,0,0,0.170587479440239,0.222795072775063,0.319919697474494,0,0,0,0,0.164188268760301,0,0,0,0,0,0,0,0,0,0,0.505877076392329,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.19352018880704,0,0,0,0.195421469921608,0.16952424724273,0,0,0,0,0,0,0.699957574123344,0,0,0,0,0,0,0.578171304839617,0.0715216048933879,0,0,0,0,0,0,0,0,0,0,0,0.178547416331584,0,0,0,0,0,0,0,0,0,0,0.0856034027394797,0.056685265411804,0.0321956448428329,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.152898414163168,0.770629967456174,0,0,0,0,0,0,0,0,0,0,0,0,0.673723670275362,0.50311262954996,0,0,0,0,0,0,0,0,0,0.34137997173303,0.268069586889531,0.294625521532408,0.437052179650614,0.200838022744453,0.513688856359159,0,0.12839024180777,0.0401101501533233,0,0.0342736005912748,0,0,0,0.149565724239018,0,0,0,0.215180180019106,0.0840229578243582,0,0.156025274855562,0,0,0.588954380766386,0.0508638757203747,0.167727230239154,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.055966461856338,0,0,0,0,0.222942499056816,0,0,0.0832161034844002,0,0.543434451171588,0,0,0,0,0.270497510320477,0,0,0,0,0,0,0,0,0,0.0685890998680107,0.381950369584154,0,0,0,0,0,0,0.62239084420464,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.167474373057587,0,0,0,0,0.191676169220254,0,0,0,0,0,0,0,0.0641946247847473,0,0,0,0,0,0,0.245909871574826,0,0,0.0845123315265278,0,0,0.146136648478548,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.115230947587976,0,0,0,0,0,0.0954388822399226,0.15309020639035,0,0,0,0,0,0.192990400359885,0.457311307048017,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0778384462202319,0.261450363437608,0.238977554911651,0.775799970507136,0,0,0,0.031493427513643,0.0797978929983786,0,0,0.173569605266192,0.339023632415484,0,0,0,0,0,0,0,0,0.179278752006845,0,0,0,0,0.0709257799838506,0,0,0,0,0.131805147259529,0.276427614232137,0.032817368032432,0,0,0,0,0,0,0,0,0,0,0.150582174035777,0.0684524727462707,0,0,0.131938013860869,0.0355151496094428,0,0.709602648459555,0.117339711759041,0.464053823959474,0.223010908997275,0.357163296394835,0.432464342404235,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.385325859198791,0.620766089761265,0.21535488492417,0,0,0,0,0,0,0,0,0,0,0,0,0,0.115932033194051,0,0.0381808373167472,0,0,0,0,0,0,0,0,0,0,0,0,0,0.127828009549688,0.0283076897745917,0.084635829807314,0.124719478691449,0.23870568380703,0.120633819454897,0,0.336004712665874,0,0,0,0,0,0
|full_id=C4726_clear_oral_giant_anaplastic_ductal_squamous_serous
|full_id=C4726_clear_oral_giant_anaplastic_ductal_squamous_serous
|id=C4726
|id=C4726

Revision as of 17:51, 12 September 2012


Full id: C4726_clear_oral_giant_anaplastic_ductal_squamous_serous



Phase1 CAGE Peaks

Hg19::chr8:128306934..128306945,-p@chr8:128306934..128306945
-
Hg19::chr8:128306960..128306989,-p@chr8:128306960..128306989
-
Hg19::chr8:128306991..128307011,-p@chr8:128306991..128307011
-


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
epithelial cell1.72e-49254
embryonic cell1.05e-28248
endo-epithelial cell5.48e-2143
animal cell3.66e-17679
eukaryotic cell3.66e-17679
mesodermal cell1.02e-16119
endodermal cell2.17e-1559
squamous epithelial cell3.90e-1462
muscle precursor cell4.53e-1157
myoblast4.53e-1157
multi-potent skeletal muscle stem cell4.53e-1157
contractile cell1.59e-1059
muscle cell3.14e-1054
native cell5.24e-10722
smooth muscle cell1.91e-0942
smooth muscle myoblast1.91e-0942
epithelial cell of alimentary canal5.44e-0921
electrically responsive cell7.75e-0960
electrically active cell7.75e-0960
endothelial cell1.46e-0835
endothelial cell of vascular tree2.27e-0824
vascular associated smooth muscle cell2.82e-0832
respiratory epithelial cell4.11e-0813
kidney cell8.80e-0818
kidney epithelial cell8.80e-0818
epithelial cell of nephron1.18e-0716
meso-epithelial cell3.57e-0744
blood vessel endothelial cell9.84e-0718
embryonic blood vessel endothelial progenitor cell9.84e-0718
Uber Anatomy
Ontology termp-valuen
mesenchyme6.06e-20238
entire embryonic mesenchyme6.06e-20238
multi-tissue structure1.12e-15347
unilaminar epithelium1.56e-14138
vasculature1.66e-1479
vascular system1.66e-1479
cell layer2.21e-14312
epithelium1.09e-13309
endoderm-derived structure1.68e-13169
endoderm1.68e-13169
presumptive endoderm1.68e-13169
trunk2.30e-13216
epithelial tube4.44e-13118
vessel8.68e-1369
respiratory system2.30e-1272
artery2.63e-1242
arterial blood vessel2.63e-1242
arterial system2.63e-1242
anatomical space3.39e-12104
blood vessel6.19e-1260
epithelial tube open at both ends6.19e-1260
blood vasculature6.19e-1260
vascular cord6.19e-1260
respiratory tract1.96e-1153
segment of respiratory tract5.42e-1146
respiratory primordium7.09e-1138
endoderm of foregut7.09e-1138
anatomical cluster7.40e-11286
anatomical system1.23e-10625
multilaminar epithelium1.43e-1082
anatomical group1.75e-10626
trunk mesenchyme2.89e-10143
multi-cellular organism3.15e-10659
mixed endoderm/mesoderm-derived structure4.17e-10130
anatomical conduit4.60e-10241
systemic artery4.99e-1033
systemic arterial system4.99e-1033
germ layer5.70e-10604
embryonic tissue5.70e-10604
presumptive structure5.70e-10604
epiblast (generic)5.70e-10604
digestive system7.70e-10155
digestive tract7.70e-10155
primitive gut7.70e-10155
embryonic structure7.98e-10605
developing anatomical structure7.98e-10605
organism subdivision9.05e-10365
immaterial anatomical entity1.64e-09126
mesoderm2.30e-09448
mesoderm-derived structure2.30e-09448
presumptive mesoderm2.30e-09448
skeletal muscle tissue2.61e-0961
striated muscle tissue2.61e-0961
myotome2.61e-0961
subdivision of digestive tract3.12e-09129
endodermal part of digestive tract3.12e-09129
embryo4.13e-09612
splanchnic layer of lateral plate mesoderm4.21e-0984
foregut4.80e-0998
muscle tissue5.87e-0963
musculature5.87e-0963
musculature of body5.87e-0963
thoracic cavity element7.91e-0934
thoracic cavity7.91e-0934
tracheobronchial tree9.55e-0914
lower respiratory tract9.55e-0914
dermomyotome9.95e-0970
organ segment1.56e-0897

Disease
Ontology termp-valuen


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
EP300#203336.77394172622320.003216880500103790.0168540073517779
FOS#235338.99795530889440.001372499272417130.00902148980502061
JUN#3725312.51282919233630.0005103313992726250.00446535698798875
JUND#372736.994663941871030.002921845042734990.0157727076248617
NR3C1#2908314.9730233311730.0002978331194675480.00310309189585707
STAT3#6774310.51946499715420.0008589184530415310.00645728363930352
TCF7L2#6934310.77017656313730.0008003181298398380.0061758848206253



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4726&oldid=2139658"