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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=1.20626728614416,1.0088692882387,1.19866292597911,0.778416444984665,0.833178629168523,0.98781749286158,0,0,0.251286965243594,0,0,0,0,0.90604840548661,0.634877498878831,0,0,0.238123940398271,0.172583317114759,0,0,0,0,0,0.176719245822362,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.205583124092593,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.101535401656103,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.40450336701766,0.478869757961344,0.622893855508333,1.37604136080859,1.33354509231382,1.35930080733611,1.11157464997718,0.644088264271259,0,0,0.0365629421359175,0.637486369740531,0,0,0,0,0,0,0,0,0,0,0,0.194599788733868,0,0,0,0.0998244934409575,0.132184822587662,0.222571133856035,0,0.245579806949268,0,0,0,0,0,0,0,0,0,0,0,0,1.05828975402871,0.84992679096007,0.850696602912822,1.14325368816681,0.62242287354656,0.739209949067075,0.315443408671468,0.348954405307274,1.24289371177915,0.394769823806012,0.646668336354939,0.848453746895271,0.830059703472599,0,0,0.196030148402437,0.060489586087507,0,0.0651586387455666,0,0.148697751957957,0,0.117263784460219,0.340047884800798,0.570535494010108,0.5717651916362,0,0.126024924791884,0,0.191486849538524,0.609897706132128,0.575001862643493,0.602576622264948,0.557379687402253,0.982755134431983,1.28222270570359,0.879089507656024,0.785440077239694,1.00739247974138,0.840465708364678,0.96327494754925,1.03972351226678,0.972183505078153,0.933133493801287,1.17584753971273,1.00918842268639,1.06633665306739,0.947368213072444,0.482119644031604,0,0,0,0,0,0,0,0,0,0,0.359167763330151,0,0.578204419255171,0.726831239021661,0,0,0,0,0,0,0,0,0,0,0,0.349223511087647,0.392712270020621,0.355556938823921,0.297284871485779,0.442851146815683,0,0.136392444904183,0.0687674306079092,0,0,0,0,0,0,0,0.535868389598166,0.200588822806923,0.156276296987917,0.165240025483351,0.29031753691091,0,0,0,0,0,0,0,0,0,0,0,0,0,0.150650916833568,0.109996748514441,0.0977724872083096,0,0,0,0,0,0,0,0.278078474225368,0.438358826582664,0.290790675513673,0.0527984507438095,0,0,0.185223678206009,0,0.0994069197460863,0,0,0.516885299161946,0,0,0.122457109962761,0.443569584031804,0,0,0,0,0,0,0,0.638963026067791,0.897171456118256,0.58576948779915,0.858873686710862,0.513249511287574,0.939500353873836,0,0,0,0,0.0983303062134256,0,0,0,0,0,0,0,0.953031890755657,0.398028867207316,0.319118576558439,0.151045379149235,0.351990019608733,0.411118488519849,0.567526581163278,0.915014783269694,0,0.308506940524756,0.476059816250789,0.191201518499852,0.378422946023144,0.337420711157552,0.307374134119775,0,0,0,0,0,0,1.15074765610866,1.34290192361368,0.903984924802973,1.12805976198365,1.21355009471417,0.78868620790649,0,0.248230446868769,0.350816122023714,0.640204413512102,0.488129996818752,0.578530231127444,0,0,0,0.164132021186938,0,0.311540966384859,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.122339886766207,0.85627325828898,0.0730357444858842,0.150003060717036,0,0,0.416114259418732,0.293739703941735,0.284270907236698,0.283532349465927,0.150298798479565,0.667666622286551,0.481476125906022,0.127398499139995,0.89517199442608,0,0,0,0,0.521690770122323,0.863099523976269,0.651780491849264,0.890797510384524,0.563662614770321,0.43772932056948,0.240872820972369,0.301436784013459,0.842268029050635,1.1251166815413,0.402268529144255,0,0.601579060626529,0.463776488052953,0,0.608294039000265,0.632906979954894,0.382692075941723,0.345000035290412,0.412477887232674,0.152673061679609,0,0.504256232200743,0.493179530162882,0.587317805545834,0.430859236571712,0.513239225317154,0,0.475717219026413,0.609504360803418,0.333961084118307,0.363948287632338,0.147929950453612,0.406389852848383,0.107784894264258,0.109518714890925,0.112184954677754,0,0.232874726698813,1.32769260978408,1.3986087792599,0,0,0,0,0,0.954349770115905,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.281701056973614,0,0,0,0,0,0,0,0,0,0,0,0,0,0.103959518714163,0,0,0,1.50595991476294,0.171855724609924,0,0,0,0,0,0.299757310563537,0.848114258232272,0,0,0,1.36016304643536,1.00506759896481,0,0,0,0.675088333183617,0,0,0,1.07374673871944,0,1.04148463187257,0.294319102417383,0.81112692815626,0,0,0,0.98677150615939,0,0,0,0,0.390585954135238,0.0695293501927681,0.563151579795656,0.576769453531076,0,0.506719447695809,0.338892655961145,0.76540616591879,0,0,1.14627051323156,0,0,0,0,0,0.282390049738061,0.185552006688486,0,0,0,0,0.143678254080772,0.125690448946222,0,0,0,0,0,0,0,0.74125687213203,0.980204420624185,0,0,0,0.955241916401606,1.46374697068709,0.697446921874945,0,0,0,0.840028645235012,0.916950758423563,0.347191613678206,1.2789404261151,0,0.0428463959634473,0,0,0,0,0,0.377806336249251,0,0,0,1.23235698562717,0,0,0,0,0.937624812716828,0.0367311208382308,1.34717753915465,0,0,0.81345016338107,0,0,0.989074666617772,0,0,0,0,0,0,0,0,0,0,0,0.342588584645784,0.762805177830736,0,0.724083624232752,0,1.71222963534683,1.66627234709803,1.07070617925649,0.25496259830806,0.269151371139379,0.818178794268689,0.83961287637731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|full_id=C4558_mature_heart_mesodermal_lung_skin_diaphragm_eye
|full_id=C4558_mature_heart_mesodermal_lung_skin_diaphragm_eye
|gostat_on_coexpression_clusters=GO:0008091!spectrin!0.0101237505259809!2037$GO:0030866!cortical actin cytoskeleton organization and biogenesis!0.0101237505259809!2037$GO:0030865!cortical cytoskeleton organization and biogenesis!0.0101237505259809!2037$GO:0030864!cortical actin cytoskeleton!0.0101237505259809!2037$GO:0030863!cortical cytoskeleton!0.012653011472308!2037$GO:0005178!integrin binding!0.0162633670782013!1842$GO:0044448!cell cortex part!0.0162633670782013!2037$GO:0005938!cell cortex!0.0202331933385269!2037$GO:0005200!structural constituent of cytoskeleton!0.0208036560891747!2037$GO:0007160!cell-matrix adhesion!0.0208036560891747!1842$GO:0032403!protein complex binding!0.0208036560891747!1842$GO:0031589!cell-substrate adhesion!0.0208036560891747!1842$GO:0019898!extrinsic to membrane!0.0208036560891747!2037$GO:0030036!actin cytoskeleton organization and biogenesis!0.0437120020465577!2037$GO:0030029!actin filament-based process!0.0437120020465577!2037$GO:0015629!actin cytoskeleton!0.0466293410899719!2037
|gostat_on_coexpression_clusters=GO:0008091!spectrin!0.0101237505259809!2037$GO:0030866!cortical actin cytoskeleton organization and biogenesis!0.0101237505259809!2037$GO:0030865!cortical cytoskeleton organization and biogenesis!0.0101237505259809!2037$GO:0030864!cortical actin cytoskeleton!0.0101237505259809!2037$GO:0030863!cortical cytoskeleton!0.012653011472308!2037$GO:0005178!integrin binding!0.0162633670782013!1842$GO:0044448!cell cortex part!0.0162633670782013!2037$GO:0005938!cell cortex!0.0202331933385269!2037$GO:0005200!structural constituent of cytoskeleton!0.0208036560891747!2037$GO:0007160!cell-matrix adhesion!0.0208036560891747!1842$GO:0032403!protein complex binding!0.0208036560891747!1842$GO:0031589!cell-substrate adhesion!0.0208036560891747!1842$GO:0019898!extrinsic to membrane!0.0208036560891747!2037$GO:0030036!actin cytoskeleton organization and biogenesis!0.0437120020465577!2037$GO:0030029!actin filament-based process!0.0437120020465577!2037$GO:0015629!actin cytoskeleton!0.0466293410899719!2037

Revision as of 17:39, 12 September 2012


Full id: C4558_mature_heart_mesodermal_lung_skin_diaphragm_eye



Phase1 CAGE Peaks

Hg19::chr6:131291472..131291492,-p2@EPB41L2
Hg19::chr6:131291507..131291537,-p6@EPB41L2
Hg19::chr9:95298256..95298282,-p1@ECM2


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:0008091spectrin0.0101237505259809
GO:0030866cortical actin cytoskeleton organization and biogenesis0.0101237505259809
GO:0030865cortical cytoskeleton organization and biogenesis0.0101237505259809
GO:0030864cortical actin cytoskeleton0.0101237505259809
GO:0030863cortical cytoskeleton0.012653011472308
GO:0005178integrin binding0.0162633670782013
GO:0044448cell cortex part0.0162633670782013
GO:0005938cell cortex0.0202331933385269
GO:0005200structural constituent of cytoskeleton0.0208036560891747
GO:0007160cell-matrix adhesion0.0208036560891747
GO:0032403protein complex binding0.0208036560891747
GO:0031589cell-substrate adhesion0.0208036560891747
GO:0019898extrinsic to membrane0.0208036560891747
GO:0030036actin cytoskeleton organization and biogenesis0.0437120020465577
GO:0030029actin filament-based process0.0437120020465577
GO:0015629actin cytoskeleton0.0466293410899719



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 cell1.44e-16180
fibroblast2.18e-1275
muscle precursor cell1.03e-0957
myoblast1.03e-0957
multi-potent skeletal muscle stem cell1.03e-0957
muscle cell7.99e-0954
contractile cell4.93e-0859
fat cell2.08e-0715
electrically responsive cell4.40e-0760
electrically active cell4.40e-0760
Uber Anatomy
Ontology termp-valuen
adult organism6.86e-31115
organism subdivision3.23e-16365
regional part of brain1.43e-1459
neural tube2.79e-1457
neural rod2.79e-1457
future spinal cord2.79e-1457
neural keel2.79e-1457
muscle tissue3.57e-1263
musculature3.57e-1263
musculature of body3.57e-1263
anatomical cluster3.59e-12286
neurectoderm5.39e-1290
anterior neural tube1.11e-1142
neural plate1.72e-1186
presumptive neural plate1.72e-1186
brain1.73e-1169
future brain1.73e-1169
anatomical conduit1.81e-11241
skeletal muscle tissue2.19e-1161
striated muscle tissue2.19e-1161
myotome2.19e-1161
central nervous system2.34e-1182
regional part of forebrain3.09e-1141
forebrain3.09e-1141
future forebrain3.09e-1141
somite3.31e-1183
paraxial mesoderm3.31e-1183
presomitic mesoderm3.31e-1183
presumptive segmental plate3.31e-1183
trunk paraxial mesoderm3.31e-1183
presumptive paraxial mesoderm3.31e-1183
multi-tissue structure5.94e-11347
tube6.63e-11194
dermomyotome1.00e-1070
multi-cellular organism1.42e-10659
cell layer1.97e-10312
regional part of nervous system4.11e-1094
nervous system4.11e-1094
epithelium4.12e-10309
telencephalon5.03e-0934
gray matter6.07e-0934
brain grey matter6.07e-0934
primary circulatory organ9.38e-0927
regional part of telencephalon1.05e-0833
heart3.92e-0824
primitive heart tube3.92e-0824
primary heart field3.92e-0824
anterior lateral plate mesoderm3.92e-0824
heart tube3.92e-0824
heart primordium3.92e-0824
cardiac mesoderm3.92e-0824
cardiogenic plate3.92e-0824
heart rudiment3.92e-0824
cerebral hemisphere4.69e-0832
anterior region of body5.70e-08129
craniocervical region5.70e-08129
splanchnic layer of lateral plate mesoderm7.82e-0884
multilaminar epithelium9.10e-0882
head2.38e-07123
anatomical system2.57e-07625
anatomical group3.60e-07626
tissue6.17e-07787
pre-chordal neural plate8.35e-0761


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

No analysis results for this cluster

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.

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