Personal tools

Coexpression cluster:C4495: 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=0.178902132573064,0.0411738202693845,0,0.210054046293455,0,0,0,0.212645603028643,0,0.0954252957357428,0,0,0,0.0960519401186186,0.124307696593413,0.370078076395268,0.523278372467957,0.393950842420822,0.295757399657426,0.0956024239401108,0.148603081231402,0.0172275286458551,0.109320656384827,0.055712496781182,0.0972869140252862,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110857771591861,0,0.17177561896448,0,0,0,0,0,0,0,0,0,0.145215606503098,0,0.0880380456512581,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.222898696087275,0.30597452061332,0.155539190226195,0,0.110486355415197,0.137424092378055,0.143451231885528,0.288997341132196,0.406898671495095,0.330789501578048,0.0534545700183436,0,0,0,0,0,0,0,0,0.660649541340769,0.724371975343731,0.65044400967576,0.642647266496382,0.5461719506012,0.660536744911173,0.545052106846428,0.790167964968339,0.721744283593036,1.05600252482121,0.95696453187989,0.606498353324642,0.645114499593944,0.837753116066459,0.703352410643561,0.891357868466129,0.875718103332284,0.87687951224857,0.748149181038026,0.759390434372195,0.717141049183282,0,0,0,0.29971293592619,0.355318379293993,0.313714019480341,0.269631976484861,0.131832994540557,0.193313197142976,0.623504608603281,0.0957506546513297,0.117672595682223,0.344862874141306,0.577359923523004,0.244719143228498,0.33291326772454,0.0914282698219536,0.210671632826821,0.433196068732539,0.277996831482617,0.101049012386207,0.171907396292758,0.193626315780556,0.259263298720939,0.0954025292462185,0.0427037663627782,0.340047884800798,0.29864956877975,0,0,0.067567801197968,0.138414987342487,0.191486849538524,0.158054039799331,0.283179832627911,0.342798473351567,0.373130235931254,0.346911488180175,0.154458903240703,0,0.278816063608295,0.11699192718931,0.248689536111648,0.137428084749711,0.224042120238607,0.250297026198814,0.177498277011549,0.136149457396536,0.386704106261293,0.131942369721337,0.363570104545418,0.178597644615193,0.248719369354389,0.189066829120808,0.109512603169101,0.0499826791869596,0.0540496261796572,0,0,0,0.13512544777972,0.363133627320823,0,0,0.165650208579294,0,0,0,0,0,0,0,0,0,0,0.393805170919361,0,0,0,0,0,0,0,0,0.342615044900017,0.0452252653904662,0,0,0.0337119464885439,0,0,0,0.258041415419499,0.360119034609418,0.556133100087439,0.378208248705171,0.745550977534197,0,0,0,0.091316660769536,0.0601805944860265,0.287205473226075,0.223217704226089,0.329235273874453,0.163719614207855,0,0,0.648227522688192,0.31314586315659,0.389395899833661,0.43607346291025,0.0977724872083096,0,0,0,0,0,0.0994533609414357,0,0.348974664770993,0.272287316351565,0.290790675513673,0.428221045560219,0,0.266067629561646,0.254744842547412,0.222676105965833,0,0,0.102578507776567,0.196428222363883,0,0,0.217871311742009,0.443569584031804,0.253326341486756,0.204900672442429,0,0.230400619595767,0,0,0,0.0932902756138882,0.33215948426107,0,0.110442433690542,0.149512438051623,0.132938760828427,0,0,0,0,0,0,0,0.0672629396841865,0,0,0,0,0.0953029273486504,0,0,0.210562647410741,0.186189563052453,0.119059432222927,0.0481081524026529,0,0,0,0.305451339051195,0.0734870933250891,0.182215346810437,0,0,0,0,0,0,0,0,0.0962521000248044,0.247312702017769,0.107433877051114,0.141267064055509,0.179467695646126,0.171012795094276,0,0.208666715931591,0.0709836812024541,0.149414895309998,0.181630511148827,0.310883002625745,0,0.146442146711949,0,0.164132021186938,0.0726509725142573,0.218961208317431,0,0.0622173525481225,0,0,0.152962663947244,0.329872362058396,0.431514462767495,0.435737264295858,0.218899063364257,0.104127248139133,0,0.0986009078228607,0,0.0535149036948416,0,0,0.179810294710844,0.123202864573785,0,0.185489220006113,0,0.0344317163371687,0,0,0,0,0.164990696339003,0.247363937051641,0.150298798479565,0.198858575654446,0.156867057756393,0.068354073672271,0.0711689110389527,0.333849019101906,0.292466594832626,0.380887461135097,0.147562287162119,0.165791835868262,0.410618958450486,0,0.208459405178838,0,0,0.284796311279533,0.234422222779115,0.325613165090915,0.289842649570622,0.402268529144255,0,0,0,0.251625724314337,0.317903523925042,0.321836143995524,0.232201568401761,0.25737372425235,0,0.496503924882133,0,0.318982817310215,0.313129023768005,0.259832572152999,0.221694345365389,0.250243980974082,0.294352089250255,0,0.157895037844406,0,0,0.0802332713627146,0.11721277736131,0.26601680365138,0.196906879012053,0.35740833319086,0.315973105304348,0,0.0831827421014,0.0304230804823102,0,0.0470365166961614,0,0,0,0.167529704189155,0,0,0,0.0898074372339897,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0922138797693087,0,0,0.108611070985339,0.0929817338882301,0,0,0,0,0.347212057654454,0,0,0.145661221236375,0.105947296040957,0,0.148934026444873,0,0.210072048745015,0.0373740412220293,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0867720438244607,0,0,0,0,0.116541676402577,0.195819502256069,0,0,0,0.214314512399756,0.135574793696297,0.315144937492197,0,0.0434059216714146,0,0,0,0,0,0,0.265759093362812,0.218254785871688,0,0,0,0.070745145653078,0,0,0,0,0.0283276594447047,0.14022092506365,0,0,0,0,0,0.273310237702706,0.0109383397674586,0.0978631351411755,0,0,0.0840016010289936,0.220626815433903,0,0,0.0837556897544824,0.0563996609564404,0.12047666065933,0,0,0.0734345958501198,0.227358067595577,0,0,0,0.0769963366386578,0,0,0.226653930460379,0.254030203224884,0,0,0.373408571052824,0.154395360924333,0,0.10762881234099,0,0.0682841300745377,0,0.175224742703361,0,0,0.118532080184479,0,0.110236269607548,0,0,0,0.155264795610224,0,0,0.0896085685791025,0.234991060098501,0.0790650569133411,0,0.052638524980514,0.150056403079832,0.499934299143301,0,0,0,0,0,0,0,0,0.0647398703344467,0.055966461856338,0,0,0,0,0,0,0.135826369078607,0.0435981622194311,0,0,0,0,0,0.188365813972295,0,0.12273585496983,0,0,0.267626937646644,0.046616925903038,0,0,0.0528027736253869,0.0539356558948951,0,0.231677263595219,0.154469515426605,0.322308240653542,0.150522826464445,0.174979787616842,0,0,0,0,0,0,0,0,0,0,0,0,0.0456863240084368,0.0261639379934246,0,0.0968963988523578,0.0613201791501264,0,0.38230436003127,0,0,0.113445166687003,0.23074003855575,0.191676169220254,0.139503167935131,0,0,0.163662235871164,0.0611624468765662,0.28614718946913,0.201784975435766,0.439690158776641,0.278663583939319,0.406987795644538,0.262311622187397,0.102379403318181,0.182341901105911,0.243357583010778,0.330903729395183,0.258575382110128,0.356588088972872,0.379547937189231,0.165551091449075,0.475740821425201,0.139255567953706,0.139715570607777,0.126050026678357,0.354463604855972,0,0,0.100713120693921,0,0.0261656084234319,0.173032754330496,0.105937148295624,0,0.364683101611907,0.349631818050522,0.141709355787741,0.0677931267972615,0,0,0.115230947587976,0,0,0,0,0,0.239879500864144,0,0,0,0,0.304339917834874,0.13615336353379,0,0,0.141036640960701,0,0,0,0,0,0,0,0,0.0921129293509972,0,0.131193766498998,0,0.0270351810347199,0,0,0,0.0976291981890722,0,0,0,0.0406607636248659,0,0,0.0474795670351238,0.140313822677655,0.376708293415585,0,0.161745814848269,0.147184609291298,0,0,0.123048870237934,0.159437324174244,0,0,0,0,0,0,0,0,0.0531531180909458,0,0,0,0.021664287542864,0.159420353662981,0,0.0687378478097941,0.0285589446518912,0,0,0.0458045054759181,0.0677256647320006,0,0.107302302820485,0,0.216899958319399,0,0.0299826682885844,0,0,0,0.139889591642163,0,0,0,0,0.339117394537181,0.388922790209006,0,0.0895896456213401,0,0.291266468109506,0.125665450581966,0,0.0202046676088652,0,0,0,0,0.166690235731849,0.0788013528114092,0,0,0,0,0.0322859259446875,0,0,0.229650884162868,0,0.0778431765528363,0,0,0.267086169465202,0.444933477630936,0.447905129199329,0,0,0.263752775583711,0,0.238130540907848,0,0,0,0,0.157260487458867,0.184415109078388,0.137352534412557,0,0.212886443495127,0.0977197726149849,0,0,0,0,0.0381808373167472,0.0971557677904766,0.0317229404497622,0,0,0,0,0,0,0,0.19330810826772,0.0758904199370637,0.147439601056333,0.00984768870535668,0.226462404668981,0.0472701757697788,0.25259680884735,0,0.148299141967317,0.0440406409639688,0.466974746384346,0,0,0.452341863994851,0.346487650381282,0,0.20515599882086,0
|full_id=C4495_Endothelial_Lymphatic_Mast_gall_Iris_osteosarcoma_Lens
|full_id=C4495_Endothelial_Lymphatic_Mast_gall_Iris_osteosarcoma_Lens
|id=C4495
|id=C4495

Revision as of 17:34, 12 September 2012


Full id: C4495_Endothelial_Lymphatic_Mast_gall_Iris_osteosarcoma_Lens



Phase1 CAGE Peaks

Hg19::chr5:34656529..34656549,+p3@RAI14
Hg19::chr5:34656551..34656562,+p8@RAI14
Hg19::chr5:34656634..34656645,+p15@RAI14


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
vasculature6.69e-3279
vascular system6.69e-3279
splanchnic layer of lateral plate mesoderm6.56e-2884
vessel3.71e-2769
blood vessel4.92e-2560
epithelial tube open at both ends4.92e-2560
blood vasculature4.92e-2560
vascular cord4.92e-2560
cardiovascular system2.93e-23110
circulatory system3.57e-22113
epithelial tube8.87e-22118
unilaminar epithelium1.35e-18138
artery1.26e-1642
arterial blood vessel1.26e-1642
arterial system1.26e-1642
somite1.32e-1683
paraxial mesoderm1.32e-1683
presomitic mesoderm1.32e-1683
presumptive segmental plate1.32e-1683
trunk paraxial mesoderm1.32e-1683
presumptive paraxial mesoderm1.32e-1683
multi-cellular organism1.69e-15659
anatomical system3.70e-15625
anatomical group7.77e-15626
trunk mesenchyme1.73e-14143
dermomyotome2.32e-1470
multilaminar epithelium1.50e-1382
anatomical cluster1.63e-13286
endothelium2.43e-1318
blood vessel endothelium2.43e-1318
cardiovascular system endothelium2.43e-1318
cell layer2.44e-13312
systemic artery4.71e-1333
systemic arterial system4.71e-1333
skeletal muscle tissue9.26e-1361
striated muscle tissue9.26e-1361
myotome9.26e-1361
muscle tissue1.23e-1263
musculature1.23e-1263
musculature of body1.23e-1263
epithelium1.54e-12309
simple squamous epithelium2.05e-1222
anatomical conduit1.99e-11241
squamous epithelium4.15e-1125
trunk5.75e-11216
aorta6.10e-1021
aortic system6.10e-1021
organism subdivision3.47e-09365
mesoderm6.79e-09448
mesoderm-derived structure6.79e-09448
presumptive mesoderm6.79e-09448
multi-tissue structure1.44e-08347
tube2.17e-08194
mesenchyme2.26e-08238
entire embryonic mesenchyme2.26e-08238
embryonic structure2.40e-08605
developing anatomical structure2.40e-08605
embryo3.23e-08612
germ layer4.21e-08604
embryonic tissue4.21e-08604
presumptive structure4.21e-08604
epiblast (generic)4.21e-08604
endothelial tube2.17e-079
arterial system endothelium2.17e-079
endothelium of artery2.17e-079
vein9.95e-079
venous blood vessel9.95e-079
venous system9.95e-079
Disease
Ontology termp-valuen
ovarian cancer8.73e-0814


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#90536.336201576962630.003930750035764890.019086131525652
CTCF#1066435.360256373075030.0064925092527670.0280914397982324
E2F1#186934.907389214879320.008460985347239390.0327134921027815
E2F4#1874312.66806031528440.0004917987006298980.00438512460472005
E2F6#187635.017155731697390.00791769806886330.032388722283264
EGR1#195834.988179094810140.008056488137383440.0322071412279498
ELF1#199734.258097958807540.01295179875054610.0464421104754612
FOS#235338.99795530889440.001372499272417130.00900788358649988
GABPB1#255337.067683836182170.002832212825417420.0154679430671846
GATA2#2624312.7449317335540.0004829527704283790.00438486519958007
HMGN3#932438.178547723350590.001827766942164210.0109055159776444
MAX#414936.452555509007120.003721913834265510.018723229080336
MYC#460935.22228187160940.007020843755740150.0295665282663607
NANOG#79923329.24477848101273.99627955670032e-050.000740013192592598
RAD21#5885310.35503389545630.0009004912073565420.00667374405372622
REST#597839.650028716128020.001112636247114590.00770370041185366
SIN3A#2594235.408884726815140.006318961977991520.0277930541174755
TAF7#6879311.43306940492390.0006690181981945830.00545020215298316
USF1#739136.361499277207960.00388404057290560.0190963804441055
USF2#7392312.99219738506960.0004558979393427810.004226302581841
YY1#752834.911170749853860.008441455341808260.0330862851626178
ZBTB7A#5134137.35190930787590.002516255860282270.0140750493166954



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:C4495&oldid=2139401"