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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.338470739899404,0.360458120508041,0.339531452985419,0.568500102648087,0.392543924306004,0.581222890308807,0,0,0,0.172634657816007,0.083204973298393,0.156216024814264,0.392981727120381,0.358562020963245,0.455565740591623,0.708596853954869,0.496263260953061,0.606530463884464,0.559291710887684,0.514339376953141,0.552681003651365,0.377172732108371,0.342583251151355,0.188030732319828,0.44098753559033,0.341227797089741,0.427338522734986,0.33476863004706,0.288156563197509,0.366711290246812,0.288687804532027,0.254820249869064,0.223799672996739,0.347200306732594,0.334480358898385,0.390377977565076,0.57594172601742,0.534761742657747,0.515861495206582,0.198772098536566,0.195175748476722,0.0059405074939124,0.352657712415373,0.182267080928499,0.409748569662144,0.406679798433519,0.327543441245195,0.27027133577128,0.897431846498752,1.08979645937415,0.861410582856643,0.648873250556035,0.657398941620516,0.6281142986568,1.1731169184784,1.11417639994209,1.0795152200886,1.23846941156093,1.15024009515852,0.995949969101773,1.16056883954868,1.10671976514757,1.13975788654327,1.07401006094827,1.12056712620076,0.969633818957923,0.889170886852779,1.01058526999358,0,0.230424741630216,0.353386002852309,0.0389944183438663,0,0.0812037792923173,0,0.052823535709485,0,0,0,0.110399020692694,0.0498827078939983,0.104078526590485,0.0306630741542676,0.0265506260076213,0,0.0304222344484003,0,0.0300251414480776,0,0,0.0233079268035905,0,0.103691217758009,0.0809973443314183,0.060050840054977,0,0,0.183314212245248,0.139258394153561,0,0.200723281844333,0.137504758249969,0.0797623568580576,0.0574444518894284,0.0327992272725087,0,0,0,0,0,0,0,0,0,0,0,0.0894731317091011,0,0,0.676360915137978,0.692989378790211,0.689413085818941,0.840152342571804,0.855609100179308,0.674079927322539,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.182538370346326,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.21624484178093,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.490013775616225,0.190815977733259,0.290795875147677,0,0,0,0,0,0,0,0,0.040912657171121,0,0.0451440091853322,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.407479865583801,0.399114709370023,0.492528432668985,0,0,0,0,0,0,0,0.209643281437639,0,0.196832087113493,0,0,0,0,0,0,0.0413832018389608,0.206375296087236,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.48681009190657,0.412179033008661,0.455650624306818,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.12688957689786,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.159177501977432,0,0,0,0,0.258349314612192,0.324825691411179,0.463364169807309,0.567701996410525,0.672306680986708,0.28947179470315,0.318076462667272,0.528836454888146,0,0,0,0.217928959998791,0.0585282132292033,0,0,0.0790289888064564,0.0760960040585542,0,0,0,0.238497174000914,0,0,0.017944479486152,0.231908151823379,0.2482912835797,0.360567482180532,0.128239398490303,0.200023105205271,0.124120355454714,0.0960361516478609,0.171802707193087,0,0,0,0,0,0,0.115279291089477,0,0.0229436725538925,0,0,0,0,0.0687832969080755,0.105030956603628,0,0,0,0.112285109921075,0.424128873830494,0,0,0.266054183028806,0,0,0,0.089714472461443,0.112581616328924,0.530818149505251,0,0,0.0562214130631495,0,0,0,0.118394496259328,0,0,0,0,0,0,0,0.165223257484438,0,0.0661608012934304,0.0206022490143138,0.0430704948946057,0,0,0.0621683679383978,0,0,0,0,0,0,0.0250361184897291,0,0,0,0,0,0,0,0,0,0,0,0,0,0.145308076513896,0.103551833417506,0,0,0,0.179228039847326,0.108667453507062,0.0914082188667263,0.135103881494694,0,0,0.144444803709627,0,0,0.258040649403603,0,0,0,0,0,0,0,0,0,0,0,0.201889650739113,0,0,0,0,0.0384981683193289,0,0,0,0,0.0250088414224685,0,0,0.0420114789121791,0,0,0,0,0,0,0,0,0,0,0,0,0.149439634110414,0.357451879411068,0,0,0.093262584852069,0.111792062755057,0,0,0,0,0.0282390906884824,0,0,0,0,0,0,0.0352989626615976,0,0.102673662120466,0,0,0,0.382456708830278,0.642702202717569,0.0248994672777727,0,0.118999338599371,0.00346186445955329,0,0,0,0,0.110327525703921,0,0,0,0,0,0,0,0,0,0.133626597701303,0.0528027736253869,0.0832875267635065,0,0,0.129456461088434,0.0910702180019836,0.372016977593597,0.464646470426371,0,0.128229312555559,0,0,0,0,0,0,0,0,0.0512262229954782,0,0.235565023413174,0.111162698252219,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.101457693038562,0.239609729499939,0.158017213582956,0.260561571466851,0,0,0,0,0.0440266644764932,0.0932409568996931,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0164828969336078,0,0,0,0.0262427864990301,0,0.100012464330829,0.0310421110538171,0,0.0145207931351988,0.116413498957969,0,0,0,0,0,0,0,0,0.0781660367096365,0,0,0,0,0,0.0141915870499514,0,0.137916903892266,0,0,0.09492163366577,0.140575750337534,0,0,0,0.0169537970073588,0,0.0890788809625826,0.0539174741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|full_id=C813_CD19_CD14CD16_CD14_Macrophage_Monocytederived_pancreatic_choriocarcinoma
|full_id=C813_CD19_CD14CD16_CD14_Macrophage_Monocytederived_pancreatic_choriocarcinoma
|gostat_on_coexpression_clusters=GO:0004558!alpha-glucosidase activity!0.0453431196630803!2595$GO:0045843!negative regulation of striated muscle development!0.0453431196630803!9734$GO:0032488!Cdc42 protein signal transduction!0.0453431196630803!221472$GO:0043088!regulation of Cdc42 GTPase activity!0.0453431196630803!221472$GO:0032489!regulation of Cdc42 protein signal transduction!0.0453431196630803!221472$GO:0032319!regulation of Rho GTPase activity!0.0453431196630803!221472$GO:0016202!regulation of striated muscle development!0.0453431196630803!9734$GO:0016566!specific transcriptional repressor activity!0.0453431196630803!9734$GO:0015926!glucosidase activity!0.0453431196630803!2595
|gostat_on_coexpression_clusters=GO:0004558!alpha-glucosidase activity!0.0453431196630803!2595$GO:0045843!negative regulation of striated muscle development!0.0453431196630803!9734$GO:0032488!Cdc42 protein signal transduction!0.0453431196630803!221472$GO:0043088!regulation of Cdc42 GTPase activity!0.0453431196630803!221472$GO:0032489!regulation of Cdc42 protein signal transduction!0.0453431196630803!221472$GO:0032319!regulation of Rho GTPase activity!0.0453431196630803!221472$GO:0016202!regulation of striated muscle development!0.0453431196630803!9734$GO:0016566!specific transcriptional repressor activity!0.0453431196630803!9734$GO:0015926!glucosidase activity!0.0453431196630803!2595

Revision as of 18:33, 12 September 2012


Full id: C813_CD19_CD14CD16_CD14_Macrophage_Monocytederived_pancreatic_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr12:109027413..109027428,-p@chr12:109027413..109027428
-
Hg19::chr15:42566384..42566475,+p2@GANC
Hg19::chr19:3178856..3178869,+p3@S1PR4
Hg19::chr1:198609269..198609281,+p@chr1:198609269..198609281
+
Hg19::chr3:46968478..46968499,-p@chr3:46968478..46968499
-
Hg19::chr4:164534657..164534701,-p1@MARCH1
Hg19::chr5:122110718..122110800,+p1@SNX2
Hg19::chr6:36973462..36973468,+p2@FGD2
Hg19::chr6:36973470..36973478,+p3@FGD2
Hg19::chr7:18330064..18330080,+p3@HDAC9


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:0004558alpha-glucosidase activity0.0453431196630803
GO:0045843negative regulation of striated muscle development0.0453431196630803
GO:0032488Cdc42 protein signal transduction0.0453431196630803
GO:0043088regulation of Cdc42 GTPase activity0.0453431196630803
GO:0032489regulation of Cdc42 protein signal transduction0.0453431196630803
GO:0032319regulation of Rho GTPase activity0.0453431196630803
GO:0016202regulation of striated muscle development0.0453431196630803
GO:0016566specific transcriptional repressor activity0.0453431196630803
GO:0015926glucosidase activity0.0453431196630803



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
leukocyte3.29e-56140
hematopoietic stem cell2.61e-53172
angioblastic mesenchymal cell2.61e-53172
nongranular leukocyte2.30e-49119
hematopoietic oligopotent progenitor cell3.29e-49165
hematopoietic multipotent progenitor cell3.29e-49165
hematopoietic lineage restricted progenitor cell1.25e-47124
hematopoietic cell3.42e-46182
myeloid leukocyte2.30e-3176
granulocyte monocyte progenitor cell3.93e-3171
macrophage dendritic cell progenitor1.61e-3065
myeloid cell1.07e-29112
common myeloid progenitor1.07e-29112
monopoietic cell2.13e-2963
monocyte2.13e-2963
monoblast2.13e-2963
promonocyte2.13e-2963
myeloid lineage restricted progenitor cell1.87e-2870
CD14-positive, CD16-negative classical monocyte1.71e-2342
classical monocyte1.10e-2245
lymphocyte3.29e-1753
common lymphoid progenitor3.29e-1753
lymphoid lineage restricted progenitor cell6.89e-1752
lymphocyte of B lineage2.58e-1224
pro-B cell2.58e-1224
B cell1.84e-0914
mesenchymal cell7.17e-09358
connective tissue cell7.09e-08365
dendritic cell2.78e-0710
intermediate monocyte4.08e-079
CD14-positive, CD16-positive monocyte4.08e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.49e-35102
blood island1.49e-35102
hemolymphoid system2.15e-32112
adult organism3.81e-28115
bone marrow1.29e-2680
bone element3.22e-2386
immune system2.18e-20115
skeletal element4.14e-19101
skeletal system4.14e-19101
neural tube1.11e-0757
neural rod1.11e-0757
future spinal cord1.11e-0757
neural keel1.11e-0757
blood1.80e-0715
haemolymphatic fluid1.80e-0715
organism substance1.80e-0715
connective tissue4.80e-07375
anterior neural tube6.33e-0742


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
EBF1#187954.45323342328450.002759080257038690.0151278655483444
IRF4#366248.765805074697650.000728667835365060.00580970608883819
NFKB1#479063.29283805451630.00391275252059270.0190696700965132
SPI1#668864.922594105113640.0004434197902305250.00412858335311454
SRF#672245.518871304867120.004058059466626480.019413662802208



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.