Personal tools

Coexpression cluster:C147: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 10:42, 17 September 2013


Full id: C147_Neutrophils_Eosinophils_CD4_CD14_CD8_Natural_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:106095687..106095690,-p@chr10:106095687..106095690
-
Hg19::chr10:11211799..11211810,+p@chr10:11211799..11211810
+
Hg19::chr10:28824063..28824067,+p10@WAC
Hg19::chr10:28830374..28830379,+p@chr10:28830374..28830379
+
Hg19::chr10:49528285..49528289,+p@chr10:49528285..49528289
+
Hg19::chr11:13692276..13692279,+p@chr11:13692276..13692279
+
Hg19::chr11:14666177..14666184,+p18@PDE3B
Hg19::chr11:14676052..14676070,+p@chr11:14676052..14676070
+
Hg19::chr11:14691257..14691272,+p@chr11:14691257..14691272
+
Hg19::chr11:14833595..14833600,+p@chr11:14833595..14833600
+
Hg19::chr11:3758544..3758552,-p@chr11:3758544..3758552
-
Hg19::chr12:92507575..92507580,-p@chr12:92507575..92507580
-
Hg19::chr12:92515098..92515120,-p@chr12:92515098..92515120
-
Hg19::chr12:92515364..92515376,-p@chr12:92515364..92515376
-
Hg19::chr12:92537471..92537501,-p2@BTG1
Hg19::chr13:41576717..41576721,-p@chr13:41576717..41576721
-
Hg19::chr13:96350060..96350064,+p@chr13:96350060..96350064
+
Hg19::chr14:21736117..21736139,-p@chr14:21736117..21736139
-
Hg19::chr14:52329716..52329721,+p@chr14:52329716..52329721
+
Hg19::chr14:52343344..52343346,+p@chr14:52343344..52343346
+
Hg19::chr14:52348441..52348445,+p@chr14:52348441..52348445
+
Hg19::chr14:55739259..55739263,+p@chr14:55739259..55739263
+
Hg19::chr14:60742581..60742585,+p@chr14:60742581..60742585
+
Hg19::chr14:65556471..65556474,-p@chr14:65556471..65556474
-
Hg19::chr14:75178739..75178742,-p@chr14:75178739..75178742
-
Hg19::chr15:63511231..63511235,+p@chr15:63511231..63511235
+
Hg19::chr15:66074183..66074186,-p@chr15:66074183..66074186
-
Hg19::chr15:72805738..72805751,+p@chr15:72805738..72805751
+
Hg19::chr15:80381625..80381629,+p@chr15:80381625..80381629
+
Hg19::chr15:93429811..93429826,+p@chr15:93429811..93429826
+
Hg19::chr15:93449913..93449918,+p@chr15:93449913..93449918
+
Hg19::chr16:48642661..48642667,-p@chr16:48642661..48642667
-
Hg19::chr16:71802092..71802096,-p@chr16:71802092..71802096
-
Hg19::chr16:81480856..81480863,+p@chr16:81480856..81480863
+
Hg19::chr16:81501508..81501512,+p@chr16:81501508..81501512
+
Hg19::chr16:9189493..9189501,+p@chr16:9189493..9189501
+
Hg19::chr17:76740925..76740928,-p@chr17:76740925..76740928
-
Hg19::chr17:8050579..8050590,-p@chr17:8050579..8050590
-
Hg19::chr17:81038499..81038502,+p@chr17:81038499..81038502
+
Hg19::chr19:1075252..1075254,+p@chr19:1075252..1075254
+
Hg19::chr19:1076513..1076515,+p@chr19:1076513..1076515
+
Hg19::chr19:15436959..15436965,-p@chr19:15436959..15436965
-
Hg19::chr19:18608622..18608626,-p@chr19:18608622..18608626
-
Hg19::chr1:156467889..156467894,-p@chr1:156467889..156467894
-
Hg19::chr1:160313765..160313770,+p@chr1:160313765..160313770
+
Hg19::chr1:182286785..182286790,-p@chr1:182286785..182286790
-
Hg19::chr1:19493205..19493209,-p@chr1:19493205..19493209
-
Hg19::chr1:198664623..198664626,+p@chr1:198664623..198664626
+
Hg19::chr1:206868829..206868837,+p@chr1:206868829..206868837
+
Hg19::chr1:22382378..22382383,+p@chr1:22382378..22382383
+
Hg19::chr1:22410852..22410856,+p@chr1:22410852..22410856
+
Hg19::chr1:247041695..247041698,-p@chr1:247041695..247041698
-
Hg19::chr1:65363369..65363374,-p@chr1:65363369..65363374
-
Hg19::chr1:67400268..67400273,+p@chr1:67400268..67400273
+
Hg19::chr20:39659128..39659131,+p@chr20:39659128..39659131
+
Hg19::chr20:43654785..43654789,+p@chr20:43654785..43654789
+
Hg19::chr20:43691658..43691663,+p@chr20:43691658..43691663
+
Hg19::chr20:5553446..5553451,-p@chr20:5553446..5553451
-
Hg19::chr21:38825079..38825081,+p@chr21:38825079..38825081
+
Hg19::chr2:136872815..136872825,-p@chr2:136872815..136872825
-
Hg19::chr2:136872943..136872964,-p@chr2:136872943..136872964
-
Hg19::chr2:144201012..144201015,+p@chr2:144201012..144201015
+
Hg19::chr2:158248047..158248055,-p@chr2:158248047..158248055
-
Hg19::chr2:174805851..174805856,-p@chr2:174805851..174805856
-
Hg19::chr2:175238488..175238492,-p@chr2:175238488..175238492
-
Hg19::chr2:197014899..197014905,-p@chr2:197014899..197014905
-
Hg19::chr2:197025997..197026001,-p@chr2:197025997..197026001
-
Hg19::chr2:201725209..201725222,-p8@CLK1
Hg19::chr2:219103332..219103343,+p3@ARPC2
Hg19::chr2:24482679..24482684,-p@chr2:24482679..24482684
-
Hg19::chr2:30371233..30371243,+p@chr2:30371233..30371243
+
Hg19::chr2:37896373..37896377,-p@chr2:37896373..37896377
-
Hg19::chr3:128471597..128471601,+p@chr3:128471597..128471601
+
Hg19::chr3:151987715..151987726,+p@chr3:151987715..151987726
+
Hg19::chr3:156869824..156869836,-p13@CCNL1
Hg19::chr3:196439003..196439007,+p10@PIGX
Hg19::chr3:63938542..63938545,+p@chr3:63938542..63938545
+
Hg19::chr3:72489507..72489512,-p@chr3:72489507..72489512
-
Hg19::chr3:72491799..72491803,-p@chr3:72491799..72491803
-
Hg19::chr3:72495585..72495599,-p@chr3:72495585..72495599
-
Hg19::chr4:69214189..69214193,-p@chr4:69214189..69214193
-
Hg19::chr5:130602669..130602672,+p@chr5:130602669..130602672
+
Hg19::chr5:130604467..130604471,+p@chr5:130604467..130604471
+
Hg19::chr5:130622100..130622104,+p@chr5:130622100..130622104
+
Hg19::chr5:130659264..130659270,+p@chr5:130659264..130659270
+
Hg19::chr5:130661190..130661194,+p@chr5:130661190..130661194
+
Hg19::chr5:78548176..78548181,+p@chr5:78548176..78548181
+
Hg19::chr5:93326321..93326326,-p@chr5:93326321..93326326
-
Hg19::chr5:98200218..98200222,-p@chr5:98200218..98200222
-
Hg19::chr5:98204026..98204029,-p@chr5:98204026..98204029
-
Hg19::chr6:136592228..136592246,-p@chr6:136592228..136592246
-
Hg19::chr6:138199611..138199623,+p@chr6:138199611..138199623
+
Hg19::chr6:139458784..139458788,+p@chr6:139458784..139458788
+
Hg19::chr6:87879071..87879073,+p@chr6:87879071..87879073
+
Hg19::chr7:104657891..104657894,+p@chr7:104657891..104657894
+
Hg19::chr7:105898066..105898077,-p@chr7:105898066..105898077
-
Hg19::chr7:106528403..106528407,+p@chr7:106528403..106528407
+
Hg19::chr7:112111642..112111647,+p@chr7:112111642..112111647
+
Hg19::chr7:130651643..130651684,-p@chr7:130651643..130651684
-
Hg19::chr7:130748590..130748596,-p@chr7:130748590..130748596
-
Hg19::chr7:130785683..130785693,-p@chr7:130785683..130785693
-
Hg19::chr7:26237801..26237806,-p@chr7:26237801..26237806
-
Hg19::chr7:5248664..5248668,+p@chr7:5248664..5248668
+
Hg19::chr7:95913127..95913131,-p@chr7:95913127..95913131
-
Hg19::chr8:101944512..101944526,-p@chr8:101944512..101944526
-
Hg19::chr8:52795373..52795379,-p@chr8:52795373..52795379
-
Hg19::chr8:53625053..53625058,-p@chr8:53625053..53625058
-
Hg19::chr8:64094817..64094823,+p@chr8:64094817..64094823
+
Hg19::chr8:68253656..68253661,-p@chr8:68253656..68253661
-
Hg19::chrX:12994880..12994894,+p6@TMSB4X
Hg19::chrX:40036135..40036145,+p@chrX:40036135..40036145
+
Hg19::chrX:40949185..40949187,+p@chrX:40949185..40949187
+
Hg19::chrX:41020910..41020914,+p@chrX:41020910..41020914
+
Hg19::chrX:41064902..41064906,+p@chrX:41064902..41064906
+
Hg19::chrX:41207753..41207764,+p@chrX:41207753..41207764
+
Hg19::chrX:44754719..44754727,+p@chrX:44754719..44754727
+
Hg19::chrY:15566813..15566817,-p@chrY:15566813..15566817
-


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:0016607nuclear speck0.0203978334575988
GO:0045603positive regulation of endothelial cell differentiation0.0203978334575988
GO:0016604nuclear body0.0203978334575988
GO:0045601regulation of endothelial cell differentiation0.020814998759357
GO:0004119cGMP-inhibited cyclic-nucleotide phosphodiesterase activity0.020814998759357
GO:0045663positive regulation of myoblast differentiation0.0260160678016211
GO:0065008regulation of biological quality0.0320032852896189
GO:0031018endocrine pancreas development0.0320032852896189
GO:0045661regulation of myoblast differentiation0.0320032852896189
GO:0005885Arp2/3 protein complex0.0320032852896189
GO:0043229intracellular organelle0.0320032852896189
GO:0043226organelle0.0320032852896189
GO:0050796regulation of insulin secretion0.0320032852896189
GO:0031016pancreas development0.0371390172926794
GO:0045446endothelial cell differentiation0.0376086394375892
GO:0045766positive regulation of angiogenesis0.0376086394375892
GO:0006928cell motility0.0376086394375892
GO:0051674localization of cell0.0376086394375892
GO:0030073insulin secretion0.0376086394375892
GO:0042593glucose homeostasis0.0376086394375892
GO:0033500carbohydrate homeostasis0.0376086394375892
GO:0003779actin binding0.0376086394375892
GO:0046883regulation of hormone secretion0.0376086394375892
GO:0030833regulation of actin filament polymerization0.0376086394375892
GO:0002790peptide secretion0.0376086394375892
GO:0030072peptide hormone secretion0.0376086394375892
GO:0044451nucleoplasm part0.0376086394375892
GO:0006479protein amino acid methylation0.0376086394375892
GO:0008213protein amino acid alkylation0.0376086394375892
GO:0005654nucleoplasm0.0419733197076172
GO:0044424intracellular part0.0419733197076172
GO:0045445myoblast differentiation0.0419733197076172
GO:0006506GPI anchor biosynthetic process0.0419733197076172
GO:0006505GPI anchor metabolic process0.0419733197076172
GO:0030041actin filament polymerization0.0419733197076172
GO:0035270endocrine system development0.0419733197076172
GO:0046879hormone secretion0.0419733197076172
GO:0008092cytoskeletal protein binding0.0419733197076172
GO:0046489phosphoinositide biosynthetic process0.0419733197076172
GO:0045765regulation of angiogenesis0.0419733197076172
GO:0015833peptide transport0.0419733197076172
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0419733197076172
GO:0048741skeletal muscle fiber development0.0419733197076172
GO:0048747muscle fiber development0.0419733197076172
GO:0044446intracellular organelle part0.0419733197076172
GO:0044422organelle part0.0419733197076172
GO:0008064regulation of actin polymerization and/or depolymerization0.0419733197076172
GO:0007010cytoskeleton organization and biogenesis0.0419733197076172
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0419733197076172
GO:0043414biopolymer methylation0.0419733197076172
GO:0031981nuclear lumen0.0419733197076172
GO:0046474glycerophospholipid biosynthetic process0.0419733197076172
GO:0042692muscle cell differentiation0.0419733197076172
GO:0030832regulation of actin filament length0.0419733197076172
GO:0045597positive regulation of cell differentiation0.0419733197076172
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0419733197076172
GO:0032535regulation of cellular component size0.0419733197076172
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0419733197076172
GO:0008283cell proliferation0.0445836578942313
GO:0006497protein amino acid lipidation0.0445836578942313
GO:0030308negative regulation of cell growth0.0445836578942313
GO:0045792negative regulation of cell size0.0445836578942313
GO:0042158lipoprotein biosynthetic process0.0445836578942313
GO:0051493regulation of cytoskeleton organization and biogenesis0.0445836578942313
GO:0033043regulation of organelle organization and biogenesis0.0445836578942313
GO:0051046regulation of secretion0.0462460849575835
GO:0008154actin polymerization and/or depolymerization0.046397908252683
GO:0045926negative regulation of growth0.046397908252683



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
leukocyte1.41e-57136
nongranular leukocyte2.29e-45115
hematopoietic lineage restricted progenitor cell3.16e-44120
hematopoietic stem cell2.41e-43168
angioblastic mesenchymal cell2.41e-43168
hematopoietic cell3.18e-42177
hematopoietic oligopotent progenitor cell1.61e-40161
hematopoietic multipotent progenitor cell1.61e-40161
myeloid leukocyte2.79e-3872
classical monocyte1.26e-3642
CD14-positive, CD16-negative classical monocyte1.26e-3642
defensive cell1.11e-3248
phagocyte1.11e-3248
granulocyte monocyte progenitor cell1.55e-3167
macrophage dendritic cell progenitor1.47e-3061
myeloid lineage restricted progenitor cell3.30e-2966
monopoietic cell5.51e-2959
monocyte5.51e-2959
monoblast5.51e-2959
promonocyte5.51e-2959
myeloid cell3.50e-25108
common myeloid progenitor3.50e-25108
lymphocyte8.27e-1453
common lymphoid progenitor8.27e-1453
lymphoid lineage restricted progenitor cell2.38e-1352
nucleate cell7.29e-1355
stuff accumulating cell1.17e-1087
intermediate monocyte1.13e-099
CD14-positive, CD16-positive monocyte1.13e-099
granulocyte2.71e-098
T cell1.85e-0825
pro-T cell1.85e-0825
blood cell1.27e-0711
CD4-positive, alpha-beta T cell1.70e-076
mature alpha-beta T cell2.80e-0718
alpha-beta T cell2.80e-0718
immature T cell2.80e-0718
mature T cell2.80e-0718
immature alpha-beta T cell2.80e-0718
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.21e-3398
blood island2.21e-3398
hemolymphoid system1.38e-29108
bone marrow2.51e-2576
immune system3.08e-2593
bone element6.53e-2382
skeletal element4.22e-1990
skeletal system1.65e-16100
lateral plate mesoderm1.07e-07203


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
MA0004.10.00584082
MA0006.10.00105075
MA0007.10.0170697
MA0009.10.536583
MA0014.15.75993e-13
MA0017.10.0246625
MA0019.10.876387
MA0024.10.039634
MA0025.10.40553
MA0027.11.37568
MA0028.10.00158629
MA0029.10.0447382
MA0030.10.0416643
MA0031.10.506613
MA0038.10.469295
MA0040.12.03804
MA0041.10.595835
MA0042.11.15734
MA0043.10.537173
MA0046.11.33163
MA0048.10.000221804
MA0050.10.478861
MA0051.10.945779
MA0052.10.402852
MA0055.11.22848e-05
MA0056.10
MA0057.11.62931e-05
MA0058.10.00464061
MA0059.10.0146339
MA0060.11.84228e-06
MA0061.10.00104528
MA0063.10
MA0066.10.0223585
MA0067.10.234997
MA0068.10.403834
MA0069.10.873586
MA0070.10.489005
MA0071.10.364504
MA0072.10.0613973
MA0073.12.40299e-07
MA0074.10.0663345
MA0076.10.00138381
MA0077.10.46723
MA0078.10.508716
MA0081.10.0760685
MA0083.10.550686
MA0084.10.9623
MA0087.11.74484
MA0088.10.00918856
MA0089.10
MA0090.10.11342
MA0091.10.060315
MA0092.10.262738
MA0093.10.000203848
MA0095.10
MA0098.10
MA0100.10.0787302
MA0101.10.0308003
MA0103.10.144068
MA0105.11.45961e-06
MA0106.10.212344
MA0107.10.00573898
MA0108.20.268105
MA0109.10
MA0111.10.505411
MA0113.10.237109
MA0114.10.000104197
MA0115.10.187748
MA0116.10.00226268
MA0117.10.0863369
MA0119.10.416216
MA0122.10.320897
MA0124.10.953765
MA0125.10.3831
MA0130.10
MA0131.10.0626589
MA0132.10
MA0133.10
MA0135.11.00057
MA0136.10.303552
MA0139.15.05956e-05
MA0140.10.0460745
MA0141.10.22038
MA0142.10.712661
MA0143.10.930182
MA0144.10.100178
MA0145.10.000217802
MA0146.19.61015e-07
MA0147.12.4157e-05
MA0148.10.427237
MA0149.10.00185726
MA0062.21.59992e-05
MA0035.20.211636
MA0039.20
MA0138.20.0548521
MA0002.20.0379598
MA0137.20.218633
MA0104.21.77046e-06
MA0047.20.350295
MA0112.20.00239019
MA0065.24.04514e-07
MA0150.10.0532543
MA0151.10
MA0152.10.803906
MA0153.11.75788
MA0154.14.51509e-06
MA0155.16.96273e-08
MA0156.10.00697494
MA0157.10.941893
MA0158.10
MA0159.10.000166418
MA0160.10.0364645
MA0161.10
MA0162.14.37515e-13
MA0163.11.04249e-09
MA0164.10.0440779
MA0080.20.0290219
MA0018.20.100234
MA0099.20.0495649
MA0079.20
MA0102.20.39615
MA0258.10.0495307
MA0259.10.00321011
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

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C147&oldid=3067265"