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{{Coexpression_clusters
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edge!0.00304382497822467!221472;51466$GO:0030036!actin cytoskeleton organization and biogenesis!0.0191085120955059!221472;51466$GO:0030029!actin filament-based process!0.0191085120955059!221472;51466$GO:0005522!profilin binding!0.0191085120955059!51466$GO:0042995!cell projection!0.0191085120955059!221472;51466$GO:0032488!Cdc42 protein signal transduction!0.0203012799919833!221472$GO:0043088!regulation of Cdc42 GTPase activity!0.0203012799919833!221472$GO:0032489!regulation of Cdc42 protein signal transduction!0.0203012799919833!221472$GO:0005246!calcium channel regulator activity!0.0221429395266416!2783$GO:0032319!regulation of Rho GTPase activity!0.0221429395266416!221472$GO:0017124!SH3 domain binding!0.0338135608774231!51466$GO:0046847!filopodium formation!0.0347714729057789!221472$GO:0030035!microspike biogenesis!0.0347714729057789!221472$GO:0007010!cytoskeleton organization and biogenesis!0.0359745203502693!221472;51466$GO:0005925!focal adhesion!0.0363003890048804!51466$GO:0016247!channel regulator activity!0.0363003890048804!2783$GO:0005924!cell-substrate adherens junction!0.0363003890048804!51466$GO:0030055!cell-matrix junction!0.0363003890048804!51466$GO:0007015!actin filament organization!0.0363003890048804!51466$GO:0022603!regulation of anatomical structure morphogenesis!0.0363003890048804!221472$GO:0022604!regulation of cell morphogenesis!0.0363003890048804!221472$GO:0008360!regulation of cell shape!0.0363003890048804!221472$GO:0001726!ruffle!0.0363003890048804!221472$GO:0030031!cell projection biogenesis!0.0405046679240081!221472$GO:0005912!adherens junction!0.0420526351365762!51466$GO:0009653!anatomical structure morphogenesis!0.0440925912246133!221472;51466$GO:0008154!actin polymerization and/or 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2;0.517858,MA0099.2;0.444294,MA0079.2;0.0313405,MA0102.2;1.36707,MA0258.1;0.155735,MA0259.1;0.191914,MA0442.1;0}}
|full_id=C780_Dendritic_CD14_CD14CD16_CD19_splenic_xeroderma_spleen
|gostat_on_coexpression_clusters=GO:0030027!lamellipodium!0.00176828189709051!221472;51466$GO:0031252!leading edge!0.00304382497822467!221472;51466$GO:0030036!actin cytoskeleton organization and biogenesis!0.0191085120955059!221472;51466$GO:0030029!actin filament-based process!0.0191085120955059!221472;51466$GO:0005522!profilin binding!0.0191085120955059!51466$GO:0042995!cell projection!0.0191085120955059!221472;51466$GO:0032488!Cdc42 protein signal transduction!0.0203012799919833!221472$GO:0043088!regulation of Cdc42 GTPase activity!0.0203012799919833!221472$GO:0032489!regulation of Cdc42 protein signal transduction!0.0203012799919833!221472$GO:0005246!calcium channel regulator activity!0.0221429395266416!2783$GO:0032319!regulation of Rho GTPase activity!0.0221429395266416!221472$GO:0017124!SH3 domain binding!0.0338135608774231!51466$GO:0046847!filopodium formation!0.0347714729057789!221472$GO:0030035!microspike biogenesis!0.0347714729057789!221472$GO:0007010!cytoskeleton organization and biogenesis!0.0359745203502693!221472;51466$GO:0005925!focal adhesion!0.0363003890048804!51466$GO:0016247!channel regulator activity!0.0363003890048804!2783$GO:0005924!cell-substrate adherens junction!0.0363003890048804!51466$GO:0030055!cell-matrix junction!0.0363003890048804!51466$GO:0007015!actin filament organization!0.0363003890048804!51466$GO:0022603!regulation of anatomical structure morphogenesis!0.0363003890048804!221472$GO:0022604!regulation of cell morphogenesis!0.0363003890048804!221472$GO:0008360!regulation of cell shape!0.0363003890048804!221472$GO:0001726!ruffle!0.0363003890048804!221472$GO:0030031!cell projection biogenesis!0.0405046679240081!221472$GO:0005912!adherens junction!0.0420526351365762!51466$GO:0009653!anatomical structure morphogenesis!0.0440925912246133!221472;51466$GO:0008154!actin polymerization and/or depolymerization!0.0440925912246133!51466
|id=C780
}}

Latest revision as of 11:30, 17 September 2013


Full id: C780_Dendritic_CD14_CD14CD16_CD19_splenic_xeroderma_spleen



Phase1 CAGE Peaks

Hg19::chr10:134146041..134146067,-p6@STK32C
Hg19::chr14:100531693..100531705,+p6@EVL
Hg19::chr17:5138099..5138164,-p1@SCIMP
Hg19::chr17:5138587..5138602,-p3@SCIMP
Hg19::chr1:112016563..112016574,+p2@C1orf162
Hg19::chr6:36973406..36973438,+p1@FGD2
Hg19::chr6:36973449..36973454,+p4@FGD2
Hg19::chr6:36996408..36996411,+p@chr6:36996408..36996411
+
Hg19::chr7:100272664..100272708,+p14@GNB2
Hg19::chr9:74920462..74920487,+p1@ENST00000451152


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:0030027lamellipodium0.00176828189709051
GO:0031252leading edge0.00304382497822467
GO:0030036actin cytoskeleton organization and biogenesis0.0191085120955059
GO:0030029actin filament-based process0.0191085120955059
GO:0005522profilin binding0.0191085120955059
GO:0042995cell projection0.0191085120955059
GO:0032488Cdc42 protein signal transduction0.0203012799919833
GO:0043088regulation of Cdc42 GTPase activity0.0203012799919833
GO:0032489regulation of Cdc42 protein signal transduction0.0203012799919833
GO:0005246calcium channel regulator activity0.0221429395266416
GO:0032319regulation of Rho GTPase activity0.0221429395266416
GO:0017124SH3 domain binding0.0338135608774231
GO:0046847filopodium formation0.0347714729057789
GO:0030035microspike biogenesis0.0347714729057789
GO:0007010cytoskeleton organization and biogenesis0.0359745203502693
GO:0005925focal adhesion0.0363003890048804
GO:0016247channel regulator activity0.0363003890048804
GO:0005924cell-substrate adherens junction0.0363003890048804
GO:0030055cell-matrix junction0.0363003890048804
GO:0007015actin filament organization0.0363003890048804
GO:0022603regulation of anatomical structure morphogenesis0.0363003890048804
GO:0022604regulation of cell morphogenesis0.0363003890048804
GO:0008360regulation of cell shape0.0363003890048804
GO:0001726ruffle0.0363003890048804
GO:0030031cell projection biogenesis0.0405046679240081
GO:0005912adherens junction0.0420526351365762
GO:0009653anatomical structure morphogenesis0.0440925912246133
GO:0008154actin polymerization and/or depolymerization0.0440925912246133



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
leukocyte1.14e-75136
nongranular leukocyte5.46e-72115
hematopoietic lineage restricted progenitor cell1.44e-67120
hematopoietic stem cell3.09e-66168
angioblastic mesenchymal cell3.09e-66168
hematopoietic oligopotent progenitor cell1.12e-61161
hematopoietic multipotent progenitor cell1.12e-61161
hematopoietic cell1.92e-60177
macrophage dendritic cell progenitor6.47e-5461
myeloid leukocyte1.90e-5372
granulocyte monocyte progenitor cell9.07e-5367
monopoietic cell1.44e-5259
monocyte1.44e-5259
monoblast1.44e-5259
promonocyte1.44e-5259
myeloid lineage restricted progenitor cell1.80e-4866
defensive cell7.79e-4648
phagocyte7.79e-4648
myeloid cell1.38e-40108
common myeloid progenitor1.38e-40108
classical monocyte2.15e-4042
CD14-positive, CD16-negative classical monocyte2.15e-4042
lymphocyte6.51e-1853
common lymphoid progenitor6.51e-1853
lymphoid lineage restricted progenitor cell1.49e-1752
nucleate cell9.59e-1755
lymphocyte of B lineage1.11e-1624
pro-B cell1.11e-1624
stuff accumulating cell2.96e-1687
B cell6.41e-1314
intermediate monocyte5.57e-119
CD14-positive, CD16-positive monocyte5.57e-119
mesenchymal cell2.08e-10354
connective tissue cell1.45e-09361
immature conventional dendritic cell8.70e-075
common dendritic progenitor8.70e-075
motile cell9.29e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.27e-5598
blood island1.27e-5598
hemolymphoid system2.00e-50108
bone marrow5.86e-4576
immune system1.67e-4293
bone element1.07e-3982
skeletal element8.01e-3490
skeletal system8.62e-29100
adult organism1.13e-26114
lateral plate mesoderm3.18e-18203
musculoskeletal system1.54e-10167
connective tissue7.73e-09371
blood3.17e-0815
haemolymphatic fluid3.17e-0815
organism substance3.17e-0815
tissue1.35e-07773


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)
MA0003.10.456919
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.0036779
MA0017.11.36636
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.014035
MA0056.10
MA0057.10.46253
MA0058.10.796055
MA0059.10.291897
MA0060.10.138988
MA0061.10.377096
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.13.47094
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.311193
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.11.44489
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.873421
MA0089.10
MA0090.10.857892
MA0091.10.382762
MA0092.10.347826
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.11.25862
MA0103.10.228129
MA0105.10.0508589
MA0106.10.516528
MA0107.10.529721
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.11.5848
MA0115.12.42332
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.109245
MA0140.11.11568
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.11.35344
MA0146.11.14011
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.366815
MA0035.20.437071
MA0039.20.138005
MA0138.20.569505
MA0002.20.80943
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.313961
MA0065.22.37156
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.729959
MA0155.11.25014
MA0156.10.715501
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.403951
MA0163.10.162989
MA0164.10.544294
MA0080.21.24809
MA0018.20.517858
MA0099.20.444294
MA0079.20.0313405
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
MA0442.10



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
BCL11A#5333538.510836531082120.004359854807656360.0206699748629907
EBF1#187954.45323342328450.002759080257038690.0151270713929794
IRF4#3662510.95725634337214.10495409675721e-050.000745595305932568
SPI1#668875.743026455965913.41922598863134e-050.000677996094601611



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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