Personal tools

Coexpression cluster:C1280: 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=0.953945576743052,1.01788535092834,0.76286227413134,1.11423709667011,0.860784370927908,0.946994633013628,0,0,0.1007790131153,0,0,0.157421329304417,0.101667003219354,0.0960519401186186,0.220838645003429,0,0,0,0.0441930753069892,0.0956024239401108,0,0.118415106013485,0,0.039279624355419,0.0513619522818629,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.640701694961298,0,0.0522561809686404,0.590118510041694,0.544897319543051,0.850251196520827,0,0.593264930303905,0.168106644744262,0.275752932992257,0.252977495828722,0.027549189648299,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.07676357717697,0.098041533233204,0.102028161711596,0.269631976484861,0,0,0,0,0,0.0548851394659095,0.122845985799448,0.0612101670326939,0,0.0914282698219536,0,0,0,0.091620887334261,0.121804624294444,0.152701773304984,0.148697751957957,0.269475635594569,0.0815818795468414,0.528403173084411,0.473944443920066,0,0,0.126024924791884,0.176228497439896,0.191486849538524,0.364913449497214,0.403538989509125,0.243333341614666,0.0887965527720659,0.982755134431983,0.645119358403725,0.463502860712094,0.398019126518488,0.405822224556558,1.13431695409988,0.656694134917761,0.744837346515477,0.469636496285367,0.981490082241632,0.530621919824733,0.360435958870614,0.90849530511988,0.231791798835545,0.178597644615193,0.0767353931304631,0,0.109512603169101,0,0,0,0,0,0,0,0.466826533052593,0,0.285272754285256,0,0.0922340184907578,0,0,0.158716988307714,0.0856043003192711,0.0402666810833727,0.0549313087713622,0,0,0,0,0,0,0,0,0,0,0,0.128119866952565,0.0861820079320161,0,0.0795639603670563,0,0.122480735257124,0,0,0,0.0916027365082372,0,0,0,0,0,0,0,0,0,0.0674361974989848,0,0.0372505621677013,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0307366208579214,0.308388040547547,0,0.266067629561646,0.314657605285744,0.488571688783462,0,0,0,0.109226104830221,0.188259409638053,0,0,0.132064901528981,0,0,0,0,0,0,0,0,0,0,0.110442433690542,0.0811586845710415,0.00454851902065745,0,0,0,0,0,0,0,0,0,0,0,0,0.136109740124972,0,0.10423609841563,0.69473207941014,0.521082727822351,0.69395198314254,0.61938744514699,0.114259303421121,0,0,0.563113368800898,0.13632043160929,0.100594818706322,0,0.128122390065496,0,0,0,0.114986933642873,0,0.114741150775265,1.01820504961828,1.36358423216594,0.98679246024862,0.649311198746593,0.821433588574408,0.98614947488475,0.598611208845803,0.116746970692643,0.13197886088098,0.0660478550963579,0,0.0907590042666714,0.0495511575604446,0.0793645050922885,0,0.164132021186938,0.134872421810318,0.0905709665096614,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00842870427678455,0,0,0,0.282326285965232,0.220127970780529,0,0,0,0.0400762477245316,0.164990696339003,0.116278029675102,0.150298798479565,0.216039547565354,0.353085884098252,0.127398499139995,0.102809556581045,0,0,0.0521599633818348,0,0,0.288793885560305,0,0,0,0,0.0738371582016079,0,0.137404238899705,0.11938108556327,0.290735813558468,0,0.268549417969833,0,0,0.18741280294663,0.504647023620096,0.288360852808394,0,0,0.152673061679609,0,0.0947203448216003,0,0.0555694062070307,0.35653234467191,0,0.190714085371158,0,0,0,0.0906424879490884,0,0.11721277736131,0,0.0582024997333375,0.173549060254662,0,0.131862706497632,0.462393313135965,0.519179906623967,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0951833797824107,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0929817338882301,0.340019274855688,0.207990005090914,0,0,0.46123552723555,0,0,0.145661221236375,0.105947296040957,0,0.080820276450175,0,0.117615805682075,0.0373740412220293,0.106148477177715,0,0.0408567533019575,0,0.324564326194432,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.106818754934198,0.0902054036215435,0.633904512625511,0,0.00483898648508602,0,0.120245177400006,0.261114907568868,0.185552006688486,0,0,0,0,0,0,0,0,0,0.065666642656593,0,0,0,0.0368115019473605,0,0,0,0,0,0.415833616916382,0,0,0,0,0.252651317607602,0,0,0.0516822929650548,0,0,0,0,0,0,0,0.0563996609564404,0.309919266601891,0.0405993330353711,0.0362531985397609,0.1301578714358,0,0.110680260976652,0.0860991584199648,0.0660391270288988,0.0769963366386578,0,0.161955095312168,0.0614277601633211,0,0,0.0775682460801064,0.0645768949458293,0,0.342197116324734,0,0,0,0,0,0,0.0553417076709348,0,0.403115931799533,0,0,0,0,0.434419073048791,0,0.106966425460878,0.0896085685791025,0.234991060098501,0,0,0,0.0282390906884824,0.318251137285304,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0329432353726146,0.0433265804049448,0.0238756131241817,0,0,0.105796722320569,0,1.18295755510842,0,0,0.089928513770318,0.53078909704316,0,0.0683298683982573,0.088711522602743,0,0,0,0,0,0,0,0.118730395337086,0.0221325846566756,0.174979787616842,0,0,0,0.291904456006495,0.0971496406207997,0.49754041697288,0,0,0,0,0,0,0,0,0,0.138284133302697,0,0,0,0,0,0.241436395256053,0.286648028920423,0.324202530144468,0.139503167935131,0.478933285450503,0.315595567788922,0.035271994063395,0.114765010550142,0.117561082617775,0,0.214098305705678,0,0.166071419879349,0.150666259251702,0.185169013863888,1.03795037028647,0.161599412638961,0.202513487587414,0.148254195206626,0.237391566872624,0.186688782225089,0.285122238562885,0.6973129570649,0.146136648478548,0.611782910213223,0.805364351358036,0,0.076502026345344,0.398129517686045,0,0.0887404631064488,0,0,0.23460721171067,0.208871915315994,0.275585725481663,0.0706617474389824,0,0.178063486278075,0,0,0.115230947587976,0,0,0,0,0.297285381790176,0.348083675621829,0,0,0,0,0,0.00776312172602064,0,0,0,0,0,0,0,0,0,0,0.549497978351569,0,0,0.382143847917994,0.952423470655296,0,0,0,0,0,0,0,0,0.0778384462202319,0,0.00733290203901252,0,0,0,0,0.0608566712043477,0,0,0,0.203321110365606,0,0,0,0,0,0,0,0.267570707282966,0,0.0988253147420914,0,0,0,0,0,0,0.268914804884285,0,0,0,0,0.032817368032432,0,0,0.281751001695877,0,0,0,0,0,0,0.287154450376049,0,0,0,0,0,0,0.153323010348428,0.163821185185472,0.117339711759041,0,0,0,0,0,0.0424427259395948,0.334416438693572,0.171934336795599,0,0,0,0,0,0,0,0.157492767753078,0,0.0952210875623146,0,0,0,0,0.6433087722433,0,0.0271284845789754,0,0,0,0,0,0,0,0,0,0,0,0.673937414748266,0.54346776659739,0.361327285921938,0,0,0,0,0,0,0,0.0317229404497622,0,0,0,0.0839445661171913,0.234059791889601,0,0,0.0878749815719147,0,0.417793352497445,0.0899220836576496,0.226462404668981,0,0.0300822291072195,0.124719478691449,0.148299141967317,0,0.466974746384346,0,0,0.135680926472736,0.258587567436989,0,0,0
|full_id=C1280_Preadipocyte_Fibroblast_Adipocyte_leiomyoblastoma_Ewing_Chondrocyte_spindle
|full_id=C1280_Preadipocyte_Fibroblast_Adipocyte_leiomyoblastoma_Ewing_Chondrocyte_spindle
|gostat_on_coexpression_clusters=GO:0005595!collagen type XII!0.00100082420817143!1303$GO:0030020!extracellular matrix structural constituent conferring tensile strength!0.00100082420817144!1303$GO:0005593!FACIT collagen!0.00200164841634287!1303$GO:0030934!anchoring collagen!0.00200164841634287!1303$GO:0030199!collagen fibril organization!0.00200164841634287!1303$GO:0030198!extracellular matrix organization and biogenesis!0.007672985595981!1303$GO:0005581!collagen!0.00772064389160821!1303$GO:0043062!extracellular structure organization and biogenesis!0.0105086541858001!1303$GO:0005201!extracellular matrix structural constituent!0.0130107147062286!1303$GO:0044420!extracellular matrix part!0.0130107147062286!1303$GO:0006817!phosphate transport!0.0130107147062286!1303$GO:0001501!skeletal development!0.0174310216256525!1303$GO:0015698!inorganic anion transport!0.0200164841634287!1303$GO:0006820!anion transport!0.0230904442313838!1303$GO:0005578!proteinaceous extracellular matrix!0.0280897994426783!1303
|gostat_on_coexpression_clusters=GO:0005595!collagen type XII!0.00100082420817143!1303$GO:0030020!extracellular matrix structural constituent conferring tensile strength!0.00100082420817144!1303$GO:0005593!FACIT collagen!0.00200164841634287!1303$GO:0030934!anchoring collagen!0.00200164841634287!1303$GO:0030199!collagen fibril organization!0.00200164841634287!1303$GO:0030198!extracellular matrix organization and biogenesis!0.007672985595981!1303$GO:0005581!collagen!0.00772064389160821!1303$GO:0043062!extracellular structure organization and biogenesis!0.0105086541858001!1303$GO:0005201!extracellular matrix structural constituent!0.0130107147062286!1303$GO:0044420!extracellular matrix part!0.0130107147062286!1303$GO:0006817!phosphate transport!0.0130107147062286!1303$GO:0001501!skeletal development!0.0174310216256525!1303$GO:0015698!inorganic anion transport!0.0200164841634287!1303$GO:0006820!anion transport!0.0230904442313838!1303$GO:0005578!proteinaceous extracellular matrix!0.0280897994426783!1303

Revision as of 13:47, 12 September 2012


Full id: C1280_Preadipocyte_Fibroblast_Adipocyte_leiomyoblastoma_Ewing_Chondrocyte_spindle



Phase1 CAGE Peaks

Hg19::chr6:75787895..75787900,-p@chr6:75787895..75787900
-
Hg19::chr6:75794459..75794475,-p2@AL359627
Hg19::chr6:75886595..75886610,-p@chr6:75886595..75886610
-
Hg19::chr6:75912479..75912515,+p@chr6:75912479..75912515
+
Hg19::chr6:75915738..75915749,-p2@COL12A1
Hg19::chr6:75915757..75915775,-p1@COL12A1
Hg19::chr6:75915872..75915881,-p3@COL12A1


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:0005595collagen type XII0.00100082420817143
GO:0030020extracellular matrix structural constituent conferring tensile strength0.00100082420817144
GO:0005593FACIT collagen0.00200164841634287
GO:0030934anchoring collagen0.00200164841634287
GO:0030199collagen fibril organization0.00200164841634287
GO:0030198extracellular matrix organization and biogenesis0.007672985595981
GO:0005581collagen0.00772064389160821
GO:0043062extracellular structure organization and biogenesis0.0105086541858001
GO:0005201extracellular matrix structural constituent0.0130107147062286
GO:0044420extracellular matrix part0.0130107147062286
GO:0006817phosphate transport0.0130107147062286
GO:0001501skeletal development0.0174310216256525
GO:0015698inorganic anion transport0.0200164841634287
GO:0006820anion transport0.0230904442313838
GO:0005578proteinaceous extracellular matrix0.0280897994426783



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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.04e-27180
fibroblast2.41e-2075
skin fibroblast3.96e-1023
muscle precursor cell9.13e-0957
myoblast9.13e-0957
multi-potent skeletal muscle stem cell9.13e-0957
muscle cell2.29e-0854
contractile cell4.25e-0859
fat cell7.87e-0815
electrically responsive cell4.64e-0760
electrically active cell4.64e-0760
stromal cell8.52e-0727
Uber Anatomy
Ontology termp-valuen
organism subdivision1.26e-18365
multi-tissue structure1.51e-14347
surface structure1.56e-1495
multi-cellular organism5.83e-14659
somite1.29e-1383
paraxial mesoderm1.29e-1383
presomitic mesoderm1.29e-1383
presumptive segmental plate1.29e-1383
trunk paraxial mesoderm1.29e-1383
presumptive paraxial mesoderm1.29e-1383
trunk mesenchyme1.98e-12143
trunk2.91e-12216
dermomyotome1.00e-1070
mesenchyme1.86e-10238
entire embryonic mesenchyme1.86e-10238
multilaminar epithelium2.01e-1082
anatomical system4.64e-10625
anatomical group8.17e-10626
muscle tissue9.66e-1063
musculature9.66e-1063
musculature of body9.66e-1063
organ1.34e-09511
skeletal muscle tissue1.49e-0961
striated muscle tissue1.49e-0961
myotome1.49e-0961
integument2.78e-0945
integumental system2.78e-0945
skin of body1.77e-0840
organ component layer2.03e-0857
organ part5.71e-07219


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
BRCA1#67238.650384561381610.003659293331202230.018475848983197
CTBP2#1488326.87871443114060.0001350903031296680.00177044750515239
GTF2F1#296235.459854661467560.0132988216841570.0470276846303133
JUN#372535.362641082429860.01397261085589020.0490582096812451
SMARCB1#659837.82259247763890.004868742725666580.0227847211330327
SMARCC1#6599318.71286827984210.0003920949266957950.0038353471995113
TFAP2A#702037.079414731304980.006452554472180970.028032376727126
TRIM28#1015537.967367876541080.004622341263156460.0218341338391134



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.