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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0587647610691441,

Latest revision as of 12:32, 17 September 2013


Full id: C3732_migratory_immature_CD14_Astrocyte_papillotubular_clear_mycosis



Phase1 CAGE Peaks

Hg19::chr18:56338688..56338708,+p1@MALT1
Hg19::chr1:995067..995099,+p1@uc009vjs.1
Hg19::chr1:995102..995125,+p1@ENST00000427998
p1@uc001acl.1


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:0032449CBM complex0.00240315553985635
GO:0002711positive regulation of T cell mediated immunity0.00240315553985635
GO:0032743positive regulation of interleukin-2 production0.00240315553985635
GO:0002726positive regulation of T cell cytokine production0.00240315553985635
GO:0002369T cell cytokine production0.00240315553985635
GO:0002724regulation of T cell cytokine production0.00240315553985635
GO:0002702positive regulation of production of molecular mediator of immune response0.00240315553985635
GO:0002720positive regulation of cytokine production during immune response0.00240315553985635
GO:0002709regulation of T cell mediated immunity0.00240315553985635
GO:0032663regulation of interleukin-2 production0.00240315553985635
GO:0002824positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.00240315553985635
GO:0002718regulation of cytokine production during immune response0.00240315553985635
GO:0002821positive regulation of adaptive immune response0.00240315553985635
GO:0002700regulation of production of molecular mediator of immune response0.00240315553985635
GO:0002367cytokine production during immune response0.00240315553985635
GO:0043621protein self-association0.00240315553985635
GO:0002705positive regulation of leukocyte mediated immunity0.00240315553985635
GO:0002456T cell mediated immunity0.00240315553985635
GO:0002708positive regulation of lymphocyte mediated immunity0.00240315553985635
GO:0002699positive regulation of immune effector process0.00240315553985635
GO:0007250activation of NF-kappaB-inducing kinase0.00240315553985635
GO:0002703regulation of leukocyte mediated immunity0.00240315553985635
GO:0002706regulation of lymphocyte mediated immunity0.00240315553985635
GO:0002819regulation of adaptive immune response0.00240315553985635
GO:0002822regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.0.00240315553985635
GO:0002697regulation of immune effector process0.00266622286226666
GO:0050852T cell receptor signaling pathway0.00290980371635028
GO:0019209kinase activator activity0.00297093404652571
GO:0032623interleukin-2 production0.0033465693857416
GO:0001819positive regulation of cytokine production0.0035431139369677
GO:0002440production of molecular mediator of immune response0.00389935093606499
GO:0050851antigen receptor-mediated signaling pathway0.00389935093606499
GO:0002429immune response-activating cell surface receptor signaling pathway0.00420132087387474
GO:0002768immune response-regulating cell surface receptor signaling pathway0.00421367769997437
GO:0002757immune response-activating signal transduction0.00422532842172546
GO:0002764immune response-regulating signal transduction0.00423633188115703
GO:0050870positive regulation of T cell activation0.00498630451083555
GO:0001817regulation of cytokine production0.00498630451083555
GO:0051168nuclear export0.00521394693065481
GO:0030693caspase activity0.00574863661035056
GO:0051251positive regulation of lymphocyte activation0.00574863661035056
GO:0050863regulation of T cell activation0.00649204106463026
GO:0051259protein oligomerization0.00666349031623854
GO:0032147activation of protein kinase activity0.00716796785828425
GO:0002253activation of immune response0.00716796785828425
GO:0002449lymphocyte mediated immunity0.00716796785828425
GO:0002250adaptive immune response0.00716796785828425
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.00716796785828425
GO:0051249regulation of lymphocyte activation0.00716796785828425
GO:0002443leukocyte mediated immunity0.00720946661956905
GO:0050865regulation of cell activation0.00724933797845053
GO:0050778positive regulation of immune response0.00749896140884057
GO:0002684positive regulation of immune system process0.00749896140884057
GO:0050776regulation of immune response0.00810781221274073
GO:0042110T cell activation0.00810781221274073
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.00810781221274073
GO:0002682regulation of immune system process0.00810781221274073
GO:0051240positive regulation of multicellular organismal process0.00836642346435401
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.00845960881044609
GO:0002252immune effector process0.00847266376231406
GO:0001816cytokine production0.00856105220692837
GO:0019207kinase regulator activity0.00909382679474178
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0100831700972994
GO:0045860positive regulation of protein kinase activity0.0100831700972994
GO:0004197cysteine-type endopeptidase activity0.0100831700972994
GO:0033674positive regulation of kinase activity0.0100831700972994
GO:0051347positive regulation of transferase activity0.010139605750829
GO:0009967positive regulation of signal transduction0.0101541783374212
GO:0006913nucleocytoplasmic transport0.0101541783374212
GO:0046649lymphocyte activation0.0101541783374212
GO:0051169nuclear transport0.0101541783374212
GO:0004842ubiquitin-protein ligase activity0.0105090574187607
GO:0008639small protein conjugating enzyme activity0.0105090574187607
GO:0006916anti-apoptosis0.0106168513974943
GO:0045321leukocyte activation0.0110914871070293
GO:0001775cell activation0.0127089956434711
GO:0043066negative regulation of apoptosis0.0136242834052795
GO:0043069negative regulation of programmed cell death0.0136273612960296
GO:0045859regulation of protein kinase activity0.0138073039089563
GO:0019787small conjugating protein ligase activity0.0138073039089563
GO:0043549regulation of kinase activity0.0138073039089563
GO:0051338regulation of transferase activity0.0139207180662411
GO:0043085positive regulation of catalytic activity0.0142541199769051
GO:0051239regulation of multicellular organismal process0.0152397913127337
GO:0008234cysteine-type peptidase activity0.0160676097141558
GO:0016881acid-amino acid ligase activity0.0160676097141558
GO:0006461protein complex assembly0.0180608506532087
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0194836255525941
GO:0007243protein kinase cascade0.0195243406003887
GO:0008047enzyme activator activity0.0233640121930479
GO:0006512ubiquitin cycle0.0278810733597028
GO:0042981regulation of apoptosis0.0286231925342692
GO:0043067regulation of programmed cell death0.0286231925342692
GO:0006952defense response0.0287120056316716
GO:0050790regulation of catalytic activity0.0294313583322489
GO:0016874ligase activity0.0311466673535068
GO:0065009regulation of a molecular function0.0319690199691438
GO:0065003macromolecular complex assembly0.0356512085583085
GO:0009966regulation of signal transduction0.0371102672789356
GO:0004175endopeptidase activity0.0371102672789356
GO:0022607cellular component assembly0.0372004084901602
GO:0006915apoptosis0.038676625753476
GO:0012501programmed cell death0.038676625753476
GO:0008219cell death0.0396747376863077
GO:0016265death0.0396747376863077
GO:0046907intracellular transport0.0396747376863077
GO:0048522positive regulation of cellular process0.0412043563088239
GO:0048518positive regulation of biological process0.0454442874524118
GO:0051649establishment of cellular localization0.0465537188207882
GO:0051641cellular localization0.0473068730398296
GO:0048523negative regulation of cellular process0.0473386668194157
GO:0048519negative regulation of biological process0.0486275006277944
GO:0006955immune response0.0486275006277944
GO:0008233peptidase activity0.0499116919816319
GO:0048468cell development0.0499116919816319



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
skeletal element3.33e-1290
bone element4.09e-1282
bone marrow2.12e-1176
skeletal system8.37e-10100
immune system1.73e-0993
hematopoietic system1.12e-0898
blood island1.12e-0898
hemolymphoid system1.21e-07108
nephron epithelium2.20e-0715
renal tubule2.20e-0715
nephron tubule2.20e-0715
nephron2.20e-0715
uriniferous tubule2.20e-0715
nephrogenic mesenchyme2.20e-0715
organ4.46e-07503
excretory tube4.79e-0716
kidney epithelium4.79e-0716
nephron tubule epithelium5.73e-0710
Disease
Ontology termp-valuen
carcinoma1.15e-11106
cell type cancer1.08e-10143
cancer2.93e-08235
disease of cellular proliferation3.39e-08239


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)
MA0003.16.06693
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.14.7105
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.28.82315
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.07067
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
MA0102.21.88331
MA0258.11.29138
MA0259.12.40872
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
CTCFL#140690213.16431623931620.007433367036996010.0306790523602777
E2F6#187635.017155731697390.00791769806886330.0322020510383587
ELF1#199734.258097958807540.01295179875054610.0462057356006245
TFAP2A#7020211.01242291536330.01054990655215560.0390122044542217
TFAP2C#7022310.80922860986020.0007916746575753130.00615741060191452
THAP1#55145220.91276306856750.002983447413736940.0158665986578711
ZEB1#6935211.25895467836260.01010222676646330.0378132915655745



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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