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Coexpression cluster:C4719: Difference between revisions

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{{Coexpression_clusters
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initiation from RNA polymerase II promoter!0.000459772037248053!6873;90390$GO:0065003!macromolecular complex assembly!0.000459772037248053!6873;8667;90390$GO:0022607!cellular component assembly!0.000459772037248053!6873;8667;90390$GO:0006352!transcription initiation!0.000536633614484254!6873;90390$GO:0016591!DNA-directed RNA polymerase II, holoenzyme!0.000686881294310163!6873;90390$GO:0003702!RNA polymerase II transcription factor activity!0.00295581685581293!6873;90390$GO:0065004!protein-DNA complex assembly!0.00295581685581293!6873;90390$GO:0044451!nucleoplasm part!0.006631102498811!6873;90390$GO:0043234!protein complex!0.00685229020748069!6873;8667;90390$GO:0005654!nucleoplasm!0.00698684889344578!6873;90390$GO:0016043!cellular component organization and biogenesis!0.00823446397347406!6873;8667;90390$GO:0006366!transcription from RNA polymerase II promoter!0.00824296163660291!6873;90390$GO:0005852!eukaryotic translation initiation factor 3 complex!0.00824296163660291!8667$GO:0031981!nuclear lumen!0.00824296163660291!6873;90390$GO:0042809!vitamin D receptor binding!0.00824296163660291!90390$GO:0016455!RNA polymerase II transcription mediator activity!0.00824296163660291!90390$GO:0010468!regulation of gene expression!0.00824296163660291!6873;8667;90390$GO:0032991!macromolecular complex!0.00824296163660291!6873;8667;90390$GO:0031323!regulation of cellular metabolic process!0.00824296163660291!6873;8667;90390$GO:0019222!regulation of metabolic process!0.00920018719068307!6873;8667;90390$GO:0000119!mediator complex!0.00933805439024332!90390$GO:0046966!thyroid hormone receptor binding!0.00968783702225466!90390$GO:0030374!ligand-dependent nuclear receptor transcription coactivator activity!0.00968783702225466!90390$GO:0031974!membrane-enclosed lumen!0.00970343980764691!6873;90390$GO:0043233!organelle lumen!0.00970343980764691!6873;90390$GO:0005669!transcription factor TFIID complex!0.0102824976655482!6873$GO:0030521!androgen receptor signaling pathway!0.0112205646551544!90390$GO:0044428!nuclear part!0.011251545384384!6873;90390$GO:0016251!general RNA polymerase II transcription factor activity!0.0125949339894161!90390$GO:0010467!gene expression!0.013924563945186!6873;8667;90390$GO:0030518!steroid hormone receptor signaling pathway!0.0140986570056485!90390$GO:0050794!regulation of cellular process!0.0140986570056485!6873;8667;90390$GO:0030522!intracellular receptor-mediated signaling pathway!0.0140986570056485!90390$GO:0035257!nuclear hormone receptor binding!0.0140986570056485!90390$GO:0006446!regulation of translational initiation!0.0140986570056485!8667$GO:0051427!hormone receptor binding!0.0140986570056485!90390$GO:0050789!regulation of biological process!0.0161097034051224!6873;8667;90390$GO:0065007!biological regulation!0.0206660733567341!6873;8667;90390$GO:0006413!translational initiation!0.022575564956508!8667$GO:0003743!translation initiation factor activity!0.0266637074945573!8667$GO:0022618!protein-RNA complex assembly!0.030115287626172!8667$GO:0006417!regulation of translation!0.0385757693507559!8667$GO:0003713!transcription coactivator activity!0.0385757693507559!90390$GO:0031326!regulation of cellular biosynthetic process!0.0396046033911602!8667$GO:0008135!translation factor activity, nucleic acid binding!0.0396046033911602!8667$GO:0005667!transcription factor complex!0.0404676791017343!6873$GO:0009889!regulation of biosynthetic process!0.0409184366965092!8667$GO:0022613!ribonucleoprotein complex biogenesis and 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097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;2.96208,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;2.26143,MA0099.2;0.902716,MA0079.2;0.181755,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4719_osteosarcoma_myelodysplastic_giant_NK_oral_small_peripheral
|gostat_on_coexpression_clusters=GO:0006367!transcription initiation from RNA polymerase II promoter!0.000459772037248053!6873;90390$GO:0065003!macromolecular complex assembly!0.000459772037248053!6873;8667;90390$GO:0022607!cellular component assembly!0.000459772037248053!6873;8667;90390$GO:0006352!transcription initiation!0.000536633614484254!6873;90390$GO:0016591!DNA-directed RNA polymerase II, holoenzyme!0.000686881294310163!6873;90390$GO:0003702!RNA polymerase II transcription factor activity!0.00295581685581293!6873;90390$GO:0065004!protein-DNA complex assembly!0.00295581685581293!6873;90390$GO:0044451!nucleoplasm part!0.006631102498811!6873;90390$GO:0043234!protein complex!0.00685229020748069!6873;8667;90390$GO:0005654!nucleoplasm!0.00698684889344578!6873;90390$GO:0016043!cellular component organization and biogenesis!0.00823446397347406!6873;8667;90390$GO:0006366!transcription from RNA polymerase II promoter!0.00824296163660291!6873;90390$GO:0005852!eukaryotic translation initiation factor 3 complex!0.00824296163660291!8667$GO:0031981!nuclear lumen!0.00824296163660291!6873;90390$GO:0042809!vitamin D receptor binding!0.00824296163660291!90390$GO:0016455!RNA polymerase II transcription mediator activity!0.00824296163660291!90390$GO:0010468!regulation of gene expression!0.00824296163660291!6873;8667;90390$GO:0032991!macromolecular complex!0.00824296163660291!6873;8667;90390$GO:0031323!regulation of cellular metabolic process!0.00824296163660291!6873;8667;90390$GO:0019222!regulation of metabolic process!0.00920018719068307!6873;8667;90390$GO:0000119!mediator complex!0.00933805439024332!90390$GO:0046966!thyroid hormone receptor binding!0.00968783702225466!90390$GO:0030374!ligand-dependent nuclear receptor transcription coactivator activity!0.00968783702225466!90390$GO:0031974!membrane-enclosed lumen!0.00970343980764691!6873;90390$GO:0043233!organelle lumen!0.00970343980764691!6873;90390$GO:0005669!transcription factor TFIID complex!0.0102824976655482!6873$GO:0030521!androgen receptor signaling pathway!0.0112205646551544!90390$GO:0044428!nuclear part!0.011251545384384!6873;90390$GO:0016251!general RNA polymerase II transcription factor activity!0.0125949339894161!90390$GO:0010467!gene expression!0.013924563945186!6873;8667;90390$GO:0030518!steroid hormone receptor signaling pathway!0.0140986570056485!90390$GO:0050794!regulation of cellular process!0.0140986570056485!6873;8667;90390$GO:0030522!intracellular receptor-mediated signaling pathway!0.0140986570056485!90390$GO:0035257!nuclear hormone receptor binding!0.0140986570056485!90390$GO:0006446!regulation of translational initiation!0.0140986570056485!8667$GO:0051427!hormone receptor binding!0.0140986570056485!90390$GO:0050789!regulation of biological process!0.0161097034051224!6873;8667;90390$GO:0065007!biological regulation!0.0206660733567341!6873;8667;90390$GO:0006413!translational initiation!0.022575564956508!8667$GO:0003743!translation initiation factor activity!0.0266637074945573!8667$GO:0022618!protein-RNA complex assembly!0.030115287626172!8667$GO:0006417!regulation of translation!0.0385757693507559!8667$GO:0003713!transcription coactivator activity!0.0385757693507559!90390$GO:0031326!regulation of cellular biosynthetic process!0.0396046033911602!8667$GO:0008135!translation factor activity, nucleic acid binding!0.0396046033911602!8667$GO:0005667!transcription factor complex!0.0404676791017343!6873$GO:0009889!regulation of biosynthetic process!0.0409184366965092!8667$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0453815620915167!8667
|id=C4719
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4719_osteosarcoma_myelodysplastic_giant_NK_oral_small_peripheral



Phase1 CAGE Peaks

Hg19::chr8:117768034..117768069,-p1@EIF3H
Hg19::chr8:118532937..118532997,+p1@MED30
Hg19::chr8:120845068..120845089,-p1@TAF2


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:0006367transcription initiation from RNA polymerase II promoter0.000459772037248053
GO:0065003macromolecular complex assembly0.000459772037248053
GO:0022607cellular component assembly0.000459772037248053
GO:0006352transcription initiation0.000536633614484254
GO:0016591DNA-directed RNA polymerase II, holoenzyme0.000686881294310163
GO:0003702RNA polymerase II transcription factor activity0.00295581685581293
GO:0065004protein-DNA complex assembly0.00295581685581293
GO:0044451nucleoplasm part0.006631102498811
GO:0043234protein complex0.00685229020748069
GO:0005654nucleoplasm0.00698684889344578
GO:0016043cellular component organization and biogenesis0.00823446397347406
GO:0006366transcription from RNA polymerase II promoter0.00824296163660291
GO:0005852eukaryotic translation initiation factor 3 complex0.00824296163660291
GO:0031981nuclear lumen0.00824296163660291
GO:0042809vitamin D receptor binding0.00824296163660291
GO:0016455RNA polymerase II transcription mediator activity0.00824296163660291
GO:0010468regulation of gene expression0.00824296163660291
GO:0032991macromolecular complex0.00824296163660291
GO:0031323regulation of cellular metabolic process0.00824296163660291
GO:0019222regulation of metabolic process0.00920018719068307
GO:0000119mediator complex0.00933805439024332
GO:0046966thyroid hormone receptor binding0.00968783702225466
GO:0030374ligand-dependent nuclear receptor transcription coactivator activity0.00968783702225466
GO:0031974membrane-enclosed lumen0.00970343980764691
GO:0043233organelle lumen0.00970343980764691
GO:0005669transcription factor TFIID complex0.0102824976655482
GO:0030521androgen receptor signaling pathway0.0112205646551544
GO:0044428nuclear part0.011251545384384
GO:0016251general RNA polymerase II transcription factor activity0.0125949339894161
GO:0010467gene expression0.013924563945186
GO:0030518steroid hormone receptor signaling pathway0.0140986570056485
GO:0050794regulation of cellular process0.0140986570056485
GO:0030522intracellular receptor-mediated signaling pathway0.0140986570056485
GO:0035257nuclear hormone receptor binding0.0140986570056485
GO:0006446regulation of translational initiation0.0140986570056485
GO:0051427hormone receptor binding0.0140986570056485
GO:0050789regulation of biological process0.0161097034051224
GO:0065007biological regulation0.0206660733567341
GO:0006413translational initiation0.022575564956508
GO:0003743translation initiation factor activity0.0266637074945573
GO:0022618protein-RNA complex assembly0.030115287626172
GO:0006417regulation of translation0.0385757693507559
GO:0003713transcription coactivator activity0.0385757693507559
GO:0031326regulation of cellular biosynthetic process0.0396046033911602
GO:0008135translation factor activity, nucleic acid binding0.0396046033911602
GO:0005667transcription factor complex0.0404676791017343
GO:0009889regulation of biosynthetic process0.0409184366965092
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0453815620915167



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>

Cell Type
Ontology termp-valuen
hematopoietic stem cell3.11e-47168
angioblastic mesenchymal cell3.11e-47168
hematopoietic cell2.15e-43177
hematopoietic oligopotent progenitor cell3.80e-43161
hematopoietic multipotent progenitor cell3.80e-43161
leukocyte2.21e-37136
nongranular leukocyte1.02e-30115
hematopoietic lineage restricted progenitor cell1.09e-30120
nucleate cell1.35e-2355
lymphocyte3.77e-2353
common lymphoid progenitor3.77e-2353
lymphoid lineage restricted progenitor cell1.15e-2252
myeloid cell7.47e-20108
common myeloid progenitor7.47e-20108
myeloid leukocyte1.01e-1272
classical monocyte6.23e-1242
CD14-positive, CD16-negative classical monocyte6.23e-1242
T cell2.16e-1125
pro-T cell2.16e-1125
lymphocyte of B lineage7.85e-1124
pro-B cell7.85e-1124
mature alpha-beta T cell2.54e-1018
alpha-beta T cell2.54e-1018
immature T cell2.54e-1018
mature T cell2.54e-1018
immature alpha-beta T cell2.54e-1018
granulocyte monocyte progenitor cell7.18e-1067
myeloid lineage restricted progenitor cell1.16e-0966
macrophage dendritic cell progenitor4.44e-0961
monopoietic cell1.31e-0859
monocyte1.31e-0859
monoblast1.31e-0859
promonocyte1.31e-0859
B cell1.92e-0814
defensive cell2.27e-0848
phagocyte2.27e-0848
mesenchymal cell2.96e-07354
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.43e-1098
blood island1.43e-1098
hemolymphoid system3.53e-09108
bone element2.22e-0882
immune system9.04e-0893
bone marrow3.61e-0776
skeletal element6.27e-0790
Disease
Ontology termp-valuen
cancer2.49e-18235
disease of cellular proliferation3.11e-17239
organ system cancer2.01e-14137
hematologic cancer1.03e-1351
immune system cancer1.03e-1351
leukemia1.60e-1139
myeloid leukemia3.62e-0931
cell type cancer3.60e-08143
carcinoma7.25e-08106


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0073.10.668628
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.31555
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
MA0131.11.06461
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.22.96208
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BRCA1#672213.45615376214920.007119807716084560.0296438206849049
ELF1#199734.258097958807540.01295179875054610.0465059791552047
ELK4#2005316.2356816584680.0002336043955745990.00256436929466213
GABPB1#255337.067683836182170.002832212825417420.0154841373226075
GTF2B#2959221.29588662288280.002878180589911410.0155909908002986
JUND#372736.994663941871030.002921845042734990.0157702622438346
NFKB1#479035.488063424193840.006049381815655430.0270887702030287
POLR3A#111281113.0440366972480.00882009881003120.0334992472041912
SIN3A#2594235.408884726815140.006318961977991520.0278352553890698
SMARCB1#6598212.16847718743830.008675002221921740.0330153981872781
YY1#752834.911170749853860.008441455341808260.0331335370731777



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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