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Coexpression cluster:C4719: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4719_osteosarcoma_myelodysplastic_giant_NK_oral_small_peripheral
|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$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0453815620915167!8667
|gostat_on_coexpression_clusters=GO:0006367!transcription initiation from RNA polymerase II promoter!0.000459772037248053!6873;90390$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

Revision as of 17:50, 12 September 2012


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 cell6.86e-48172
angioblastic mesenchymal cell6.86e-48172
hematopoietic oligopotent progenitor cell7.71e-44165
hematopoietic multipotent progenitor cell7.71e-44165
hematopoietic cell7.57e-43182
leukocyte3.22e-38140
nongranular leukocyte4.10e-32119
hematopoietic lineage restricted progenitor cell5.33e-32124
lymphocyte7.19e-2353
common lymphoid progenitor7.19e-2353
lymphoid lineage restricted progenitor cell2.79e-2252
myeloid cell1.25e-20112
common myeloid progenitor1.25e-20112
myeloid leukocyte2.98e-1376
CD14-positive, CD16-negative classical monocyte4.08e-1342
classical monocyte4.22e-1345
T cell1.53e-1125
pro-T cell1.53e-1125
granulocyte monocyte progenitor cell5.07e-1171
myeloid lineage restricted progenitor cell6.83e-1170
lymphocyte of B lineage1.39e-1024
pro-B cell1.39e-1024
macrophage dendritic cell progenitor2.12e-1065
mature alpha-beta T cell2.38e-1018
alpha-beta T cell2.38e-1018
immature T cell2.38e-1018
mature T cell2.38e-1018
immature alpha-beta T cell2.38e-1018
monopoietic cell6.75e-1063
monocyte6.75e-1063
monoblast6.75e-1063
promonocyte6.75e-1063
B cell2.18e-0814
mesenchymal cell1.66e-07358
motile cell7.76e-07390
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.21e-12102
blood island3.21e-12102
hemolymphoid system1.74e-10112
bone element8.31e-1086
bone marrow1.67e-0880
skeletal element1.93e-07101
skeletal system1.93e-07101
connective tissue3.06e-07375
Disease
Ontology termp-valuen
cancer1.20e-18235
disease of cellular proliferation1.73e-17239
organ system cancer1.66e-14137
hematologic cancer1.21e-1351
immune system cancer1.21e-1351
leukemia8.12e-1239
myeloid leukemia4.91e-0931
cell type cancer6.18e-09143
carcinoma2.74e-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)

{{{tfbs_overrepresentation_jaspar}}}



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.