Personal tools

Coexpression cluster:C3994: 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=0,0,0,0,0,0,0,0.212645603028643,0,0.472152329592188,0,0,0,0.0506760246065907,0,0,0.204850754147253,0.238123940398271,0,0.0504265701716883,0,0.118415106013485,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.141006687969447,0,0,0,0,0,0.0392295810357272,0,0.101576743883372,0.235625625896777,0,0,0,0,0,0,0,0,0,0,0,0,0.152135224370875,0,0,0,0.315403250032236,0.12539036754857,0.416859640708625,0,0,0,0,0.160318030086386,0.087969206950705,0.0463435368962281,0,0,0,0,0,0,0,0.0517815087208527,0.0540033816753664,0.109523411542048,0.232827633528851,0.428464084834487,0,0.0957506546513297,0.210163845666834,0.10360579629716,0.420717824619621,0.0612101670326939,0,0.231205542601898,0,0,0,0.0482220752390542,0.0651586387455666,0.107515772682637,0,0.0503156775564332,0,0.340047884800798,0.39508192670348,0,0,0.067567801197968,0.0511982733942606,0,0,0,0.312106748713396,0.305542599323342,0.133148912944135,0.084060318828564,0,0.278816063608295,0.180487917264505,0,0.074127477864629,0.371106791410596,0.225841234395813,0,0.105901621330139,0.216583950963676,0.131942369721337,0.205343129016856,0.068022726550833,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.149703653910611,0.392712270020621,0.355556938823921,0,0,0,0,0.128119866952565,0,0,0,0,0.296100002047877,0,0,0.129622621258172,0.131049308664644,0,0,0,0,0,0,0,0,0,0,0.0575805665668305,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.157142363216531,0,0.142331623276272,0,0,0,0,0,0,0.102578507776567,0.109226104830221,0,0.260843920469556,0,0.132064901528981,0.253326341486756,0.279739502385768,0.43823640236081,0.414901158706229,0,0,0,0,0,0,0.0587225291397336,0,0.0715362608323278,0,0,0,0,0.356116364892922,0,0.248779474225184,0.0672629396841865,0,0,0,0,0.0502604313716981,0.176140627153145,0.10423609841563,0,0,0,0,0.204633286556638,0,0,0.367067139814408,0.13632043160929,0.0695819800362469,0.143515142523472,0.128122390065496,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0622847174750899,0,0.123364377991644,0.407860349498638,0.0907590042666714,0,0,0,0.164132021186938,0,0.0535103765953433,0,0,0,0,0.0435790287959822,0,0.483034194766346,0,0,0.104127248139133,0,0,0,0,0,0,0,0,0.122339886766207,0.180471411475361,0,0,0,0,0,0.141977151642548,0.248032906742817,0.116278029675102,0.0560798888033103,0.0845192582018698,0.156867057756393,0.0988789363017444,0.132300728608495,0,0,0,0,0,0,0.229691380353826,0.284227806740343,0,0,0.0738371582016079,0.155146078715492,0,0.11938108556327,0.196422311813607,0.0989542966657617,0.268549417969833,0.213891194797874,0,0.133457443424548,0.260932224442006,0.0483689238882358,0.147479985915863,0,0.152673061679609,0,0.469779013844766,0,0.0555694062070307,0.108162629238214,0.64248860843547,0.505890548001969,0.475717219026413,0.364617148609597,0.198320387665648,0,0.147929950453612,0.406389852848383,0.327723059759728,0.331890866951329,0.2012589601207,0.23384408718912,0,0.0831827421014,0.123621336231306,0.139713259292333,0,0,0,0,0.167529704189155,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.107480362063099,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0745021362340714,0,0,0,0,0,0,0,0,0.0571597974145305,0.0458347162451775,0,0,0.254546132326747,0,0,0,0,0,0,0,0,0.112581616328924,0,0,0.294319102417383,0.0739148182245154,0,0,0,0.236788992518656,0,0,0,0,0,0,0,0.484319696350435,0,0,0,0.273589565652958,0,0,0.266338220705595,0.0891573798126359,0,0,0,0,0,0,0,0,0,0,0,0.0673764988462845,0,0,0,0,0,0,0,0.070745145653078,0,0,0,0,0.14749292295537,0,0.0914082188667263,0,0,0,0,0.344374029099016,0,0.119233744361939,0,0,0,0,0,0,0,0,0,0,0,0.230169522172044,0,0,0,0,0.0402022792589852,0,0.0884836478019413,0,0,0.0517780703133839,0,0,0.600792383932955,0,0,0,0.128137448453047,0,0,0.0919109500998384,0.69383436428105,0.532227488934181,0,0,0.204234048342335,0.0557243212092205,0,0.155264795610224,0,0.264309401882715,0.331589670039496,0,0.0790650569133411,0.155100922768919,0.325486371554238,0.186806023204562,0,0,0,0,0,0.144172393115712,0,0,0.104625985571293,0,0,0,0,0,0.153890104025735,0,0.289068845040772,0.0433265804049448,0.0832161034844002,0,0,0.234186964128339,0.562098623744493,0,0,0,0.218318755578087,0,0,0,0,0.158258943052669,0,0.24936904150054,0.253676102438086,0,0,0.084066558699748,0.0634100406668813,0,0,0,0,0,0,0,0,0,0,0,0.135475749945113,0.0512262229954782,0.196841684047034,0.124760798356953,0.241834462609344,0,0,0,0,0,0,0,0.0604163273998613,0,0,0.195403946339443,0.244203793146463,0.443985809596691,0.226991548579056,0.114765010550142,0.350925610181762,0.27580202584006,0.325326258620212,0,0.522306535521782,0.42468972609494,0.254674973982594,0,0.0607951148206197,0.140132417719247,0.346472721415205,0.237391566872624,0.526731032664918,0,0,0,0,0.126050026678357,0,0,0,0,0,0,0,0.132956589778862,0,0,0,0,0,0,0,0,0.0562408777463757,0,0,0,0,0.0954388822399226,0,0,0,0,0,0,0,0,0.0522684293388448,0,0.0634331720967665,0,0,0.0837085814034122,0,0,0,0,0,0,0,0.589984782145904,0,0,0.0810289837637627,0,0.0562622698659916,0,0,0,0,0,0,0,0,0,0.991208722040119,0,0.755042351369731,0,0,0,0.0283831740999027,0,0,0.0518590253631363,0,0,0,0,0,0,0,1.11857262811377,1.07655980902735,0,0,0,0.0805937328599224,0.0276646214758744,0,0,0.270311689669048,0.88963614107986,0,0,0,0,0.345393582363585,0,0,0,0,0,0,0,0,0.092251718923439,0.0683442610773682,0,0,0,0,0,0,0,0,0.081104385612865,0,0,0,0,0,0,0,0,0.0322859259446875,0,0,0.0952210875623146,0,0,0.112955512742184,0,0.0681588064684956,0.167293577865052,0.0526615420969484,0,0,0,0,0,0,0,0,0.104475489260261,0.157260487458867,0.313456698449451,0.241543999416652,0.164999540860188,0,0,0,0,0,0,0,0,0.184819397560959,0.103106967823645,0.262253936867136,0.0427459664864042,0.0839445661171913,0,0.0271819376754428,0.0261550693490902,0,0.160027141720365,0,0.0855462791577618,0.226462404668981,0.0799247580103784,0.234826457397195,0,0,0,0,0,0,0.094988929438441,0,0.367637943472982,0,0
|full_id=C3994_pituitary_ovary_putamen_pancreas_glioblastoma_Smooth_gall
|full_id=C3994_pituitary_ovary_putamen_pancreas_glioblastoma_Smooth_gall
|id=C3994
|id=C3994

Revision as of 17:00, 12 September 2012


Full id: C3994_pituitary_ovary_putamen_pancreas_glioblastoma_Smooth_gall



Phase1 CAGE Peaks

Hg19::chr1:68516345..68516360,-p4@DIRAS3
Hg19::chr1:68516361..68516380,-p3@DIRAS3
Hg19::chr1:68516393..68516402,-p6@DIRAS3


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
anatomical cluster2.04e-22286
anatomical conduit1.43e-21241
epithelium4.39e-20309
tube5.18e-20194
cell layer6.99e-20312
multi-tissue structure8.28e-19347
adult organism3.65e-18115
organism subdivision3.10e-16365
splanchnic layer of lateral plate mesoderm6.27e-1684
muscle tissue8.92e-1563
musculature8.92e-1563
musculature of body8.92e-1563
epithelial tube1.38e-14118
skeletal muscle tissue1.72e-1461
striated muscle tissue1.72e-1461
myotome1.72e-1461
circulatory system4.99e-14113
vasculature1.01e-1379
vascular system1.01e-1379
anatomical group5.63e-13626
somite6.05e-1383
paraxial mesoderm6.05e-1383
presomitic mesoderm6.05e-1383
presumptive segmental plate6.05e-1383
trunk paraxial mesoderm6.05e-1383
presumptive paraxial mesoderm6.05e-1383
cardiovascular system6.44e-13110
dermomyotome7.10e-1370
neural plate8.04e-1386
presumptive neural plate8.04e-1386
anatomical system8.58e-13625
multi-cellular organism1.81e-12659
vessel3.21e-1269
trunk mesenchyme5.20e-12143
neurectoderm6.57e-1290
blood vessel1.37e-1160
epithelial tube open at both ends1.37e-1160
blood vasculature1.37e-1160
vascular cord1.37e-1160
primary circulatory organ3.80e-1127
multilaminar epithelium1.40e-1082
artery1.64e-1042
arterial blood vessel1.64e-1042
arterial system1.64e-1042
unilaminar epithelium3.31e-10138
heart9.04e-1024
primitive heart tube9.04e-1024
primary heart field9.04e-1024
anterior lateral plate mesoderm9.04e-1024
heart tube9.04e-1024
heart primordium9.04e-1024
cardiac mesoderm9.04e-1024
cardiogenic plate9.04e-1024
heart rudiment9.04e-1024
head1.71e-09123
central nervous system1.78e-0982
anterior region of body2.46e-09129
craniocervical region2.46e-09129
regional part of nervous system3.14e-0994
nervous system3.14e-0994
neural tube4.47e-0957
neural rod4.47e-0957
future spinal cord4.47e-0957
neural keel4.47e-0957
germ layer1.66e-08604
embryonic tissue1.66e-08604
presumptive structure1.66e-08604
epiblast (generic)1.66e-08604
embryonic structure2.23e-08605
developing anatomical structure2.23e-08605
regional part of brain2.42e-0859
embryo4.44e-08612
pre-chordal neural plate4.60e-0861
brain5.20e-0869
future brain5.20e-0869
compound organ2.15e-0769
systemic artery2.89e-0733
systemic arterial system2.89e-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
CEBPB#105137.971147625824820.001974187055288560.0115307936842057
EGR1#195834.988179094810140.008056488137383440.0321014674976227



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:C3994&oldid=2138844"