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Coexpression cluster:C806: Difference between revisions

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{{Coexpression_clusters
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channel activity!0.0291262085968781!1186;219931$GO:0005244!voltage-gated ion channel activity!0.0291262085968781!1186;219931$GO:0005031!tumor necrosis factor receptor activity!0.0291262085968781!8764$GO:0043120!tumor necrosis factor binding!0.0291262085968781!8764$GO:0005035!death receptor activity!0.0291262085968781!8764$GO:0022836!gated channel activity!0.0353237716946849!1186;219931$GO:0005216!ion channel activity!0.0400503140713481!1186;219931$GO:0022838!substrate specific channel activity!0.0400503140713481!1186;219931$GO:0022803!passive transmembrane transporter activity!0.0400503140713481!1186;219931$GO:0015267!channel activity!0.0400503140713481!1186;219931$GO:0000794!condensed nuclear chromosome!0.0401184445550083!6002$GO:0008277!regulation of G-protein coupled receptor protein signaling pathway!0.0401184445550083!6002$GO:0005247!voltage-gated chloride channel activity!0.0401184445550083!1186$GO:0022844!voltage-gated anion channel activity!0.0401184445550083!1186$GO:0016021!integral to membrane!0.0401184445550083!1186;26175;8764;219931$GO:0031224!intrinsic to membrane!0.0401184445550083!1186;26175;8764;219931$GO:0000793!condensed chromosome!0.0444359502873847!6002$GO:0043168!anion binding!0.0458535690852464!1186$GO:0031404!chloride ion 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|full_id=C806_Melanocyte_CD14_Monocytederived_Macrophage_granulocyte_Mast_Eosinophils
|id=C806
}}

Latest revision as of 11:31, 17 September 2013


Full id: C806_Melanocyte_CD14_Monocytederived_Macrophage_granulocyte_Mast_Eosinophils



Phase1 CAGE Peaks

Hg19::chr11:68816311..68816323,+p3@TPCN2
Hg19::chr11:68816334..68816353,+p2@TPCN2
Hg19::chr11:68816356..68816464,+p1@TPCN2
Hg19::chr14:93651358..93651412,+p1@C14orf109
Hg19::chr16:1524969..1525015,-p2@CLCN7
Hg19::chr1:2487325..2487330,+p15@TNFRSF14
Hg19::chr1:2487402..2487416,+p5@TNFRSF14
Hg19::chr1:2487548..2487559,+p11@TNFRSF14
Hg19::chr1:2487562..2487573,+p8@TNFRSF14
Hg19::chr4:3387396..3387446,+p4@RGS12


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:0022832voltage-gated channel activity0.0291262085968781
GO:0005244voltage-gated ion channel activity0.0291262085968781
GO:0005031tumor necrosis factor receptor activity0.0291262085968781
GO:0043120tumor necrosis factor binding0.0291262085968781
GO:0005035death receptor activity0.0291262085968781
GO:0022836gated channel activity0.0353237716946849
GO:0005216ion channel activity0.0400503140713481
GO:0022838substrate specific channel activity0.0400503140713481
GO:0022803passive transmembrane transporter activity0.0400503140713481
GO:0015267channel activity0.0400503140713481
GO:0000794condensed nuclear chromosome0.0401184445550083
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.0401184445550083
GO:0005247voltage-gated chloride channel activity0.0401184445550083
GO:0022844voltage-gated anion channel activity0.0401184445550083
GO:0016021integral to membrane0.0401184445550083
GO:0031224intrinsic to membrane0.0401184445550083
GO:0000793condensed chromosome0.0444359502873847
GO:0043168anion binding0.0458535690852464
GO:0031404chloride ion binding0.0458535690852464



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
myeloid leukocyte1.17e-4472
granulocyte monocyte progenitor cell1.06e-4067
macrophage dendritic cell progenitor2.01e-3961
myeloid lineage restricted progenitor cell4.30e-3966
monopoietic cell1.07e-3859
monocyte1.07e-3859
monoblast1.07e-3859
promonocyte1.07e-3859
defensive cell1.80e-3848
phagocyte1.80e-3848
classical monocyte1.15e-3342
CD14-positive, CD16-negative classical monocyte1.15e-3342
leukocyte2.38e-32136
myeloid cell3.39e-31108
common myeloid progenitor3.39e-31108
hematopoietic lineage restricted progenitor cell1.32e-26120
hematopoietic stem cell6.19e-26168
angioblastic mesenchymal cell6.19e-26168
hematopoietic cell7.61e-26177
nongranular leukocyte8.17e-26115
stuff accumulating cell1.43e-2587
hematopoietic oligopotent progenitor cell3.26e-24161
hematopoietic multipotent progenitor cell3.26e-24161
intermediate monocyte7.15e-089
CD14-positive, CD16-positive monocyte7.15e-089
Uber Anatomy
Ontology termp-valuen
hemolymphoid system7.38e-37108
hematopoietic system9.19e-3798
blood island9.19e-3798
immune system1.32e-3593
bone marrow4.81e-3576
bone element3.26e-3282
skeletal element4.35e-2790
skeletal system6.73e-21100
lateral plate mesoderm7.40e-14203
adult organism5.35e-09114


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)
MA0003.11.07531
MA0004.11.75693
MA0006.11.23783
MA0007.10.952442
MA0009.10.828613
MA0014.11.9973
MA0017.11.36636
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.11.99525
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
MA0048.11.25863
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.802927
MA0058.13.07259
MA0059.10.79343
MA0060.10.848451
MA0061.10.377096
MA0063.10
MA0066.14.18732
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.0824235
MA0074.11.19015
MA0076.11.50024
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.873421
MA0089.10
MA0090.10.857892
MA0091.10.382762
MA0092.10.347826
MA0093.13.56644
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.678051
MA0103.10.646502
MA0105.10.422512
MA0106.10.516528
MA0107.11.01551
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.998594
MA0115.11.06753
MA0116.13.07162
MA0117.12.01191
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
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.11.54256
MA0143.10.532484
MA0144.11.51733
MA0145.11.81958
MA0146.10.243477
MA0147.11.03863
MA0148.10.403564
MA0149.10.428597
MA0062.21.77242
MA0035.20.437071
MA0039.26.16702
MA0138.20.569505
MA0002.20.80943
MA0137.20.255808
MA0104.21.36686
MA0047.20.504873
MA0112.24.04027
MA0065.20.147044
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.12.09876
MA0155.10.12484
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.11.04074
MA0160.10.417847
MA0161.10
MA0162.10.631119
MA0163.12.94358
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.22.76826
MA0102.21.36707
MA0258.12.11165
MA0259.10.560522
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
BATF#1053849.743120716921450.0004882890842555010.00436650600826786
BCL11A#5333538.510836531082120.004359854807656360.020670913213039
BHLHE40#8553313.46154406409320.001180108215232760.0080073623889484
CCNT2#90553.168100788481320.01227157669794290.0444794613297863
E2F6#187663.010293439018430.006255795847314780.0276047432185951
FOS#235387.198364247115538.49742894810215e-073.69160974172563e-05
HMGN3#932454.08927386167530.004038023271587280.0193337510870263
MAFK#797538.130219941348970.004957565697075180.0231619935509007
MAX#414953.226277754503560.01135492218371950.0416294000051069
NFE2#4778538.60213032581458.66761903293144e-085.14339468284276e-06
NFKB1#479063.29283805451630.00391275252059270.0190687802378992
NRF1#489944.884111779084360.00630934732180550.0278269393978904
PAX5#507953.334782765588910.009853624493675830.0370300704722756
POLR2A#5430102.147453176558070.0004793377491637920.00436418404541167
USF1#739163.816899566324770.001780928663791640.0109275840854084
USF2#739256.49609869253480.0004890967532056060.00437335409315413



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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