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Coexpression cluster:C3185: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0050760!negative regulation of thymidylate synthase biosynthetic process!0.00237450449389693!322$GO:0050758!regulation of thymidylate synthase biosynthetic process!0.00237450449389693!322$GO:0050757!thymidylate synthase biosynthetic process!0.00237450449389693!322$GO:0045749!negative regulation of S phase of mitotic cell cycle!0.0123009907713758!322$GO:0001540!beta-amyloid binding!0.0123009907713758!322$GO:0007090!regulation of S phase of mitotic cell cycle!0.0123009907713758!322$GO:0045930!negative regulation of progression through mitotic cell cycle!0.0123009907713758!322$GO:0033261!regulation of progression through S phase!0.0123009907713758!322$GO:0000084!S phase of mitotic cell cycle!0.0123009907713758!322$GO:0030426!growth cone!0.0123009907713758!322$GO:0030427!site of polarized growth!0.0123009907713758!322$GO:0051320!S phase!0.0124624789486762!322$GO:0007346!regulation of progression through mitotic cell cycle!0.0175268017854181!322$GO:0030027!lamellipodium!0.0194594735801954!322$GO:0017148!negative regulation of translation!0.0194594735801954!322$GO:0031327!negative regulation of cellular biosynthetic process!0.0200219068535414!322$GO:0009890!negative regulation of biosynthetic process!0.0202299818924186!322$GO:0030308!negative regulation of cell growth!0.0202299818924186!322$GO:0045792!negative regulation of cell size!0.0202299818924186!322$GO:0045926!negative regulation of growth!0.0217075291219072!322$GO:0031252!leading edge!0.0243979520439284!322$GO:0051329!interphase of mitotic cell cycle!0.0274886381140926!322$GO:0051325!interphase!0.0275265936430817!322$GO:0009615!response to virus!0.0275265936430817!51561$GO:0007050!cell cycle arrest!0.0275265936430817!322$GO:0051248!negative regulation of protein metabolic process!0.0275265936430817!322$GO:0048771!tissue remodeling!0.0275265936430817!51561$GO:0007409!axonogenesis!0.0275265936430817!322$GO:0045087!innate immune response!0.0275265936430817!51561$GO:0048667!neuron morphogenesis during differentiation!0.0275265936430817!322$GO:0048812!neurite morphogenesis!0.0275265936430817!322$GO:0000904!cellular morphogenesis during differentiation!0.0279972299614313!322$GO:0031175!neurite development!0.0290841708536053!322$GO:0048666!neuron development!0.0321926668132127!322$GO:0001558!regulation of cell growth!0.0327848518702859!322$GO:0006417!regulation of translation!0.0327848518702859!322$GO:0031326!regulation of cellular biosynthetic process!0.0327848518702859!322$GO:0016049!cell growth!0.0327848518702859!322$GO:0040008!regulation of growth!0.0327848518702859!322$GO:0032990!cell part morphogenesis!0.0327848518702859!322$GO:0030030!cell projection organization and biogenesis!0.0327848518702859!322$GO:0048858!cell projection morphogenesis!0.0327848518702859!322$GO:0008361!regulation of cell size!0.0327848518702859!322$GO:0051707!response to other organism!0.0327848518702859!51561$GO:0030182!neuron differentiation!0.0327848518702859!322$GO:0032501!multicellular organismal process!0.0327848518702859!322;51561$GO:0009889!regulation of biosynthetic process!0.0327848518702859!322$GO:0045786!negative regulation of progression through cell cycle!0.0332813801169429!322$GO:0048699!generation of neurons!0.0350566403475582!322$GO:0022008!neurogenesis!0.0371838177210064!322$GO:0009607!response to biotic stimulus!0.0396941228186807!51561$GO:0006954!inflammatory response!0.0396941228186807!51561$GO:0005125!cytokine activity!0.0411003848729342!51561$GO:0042995!cell projection!0.0411003848729342!322$GO:0000278!mitotic cell cycle!0.0420210337736801!322$GO:0051704!multi-organism process!0.0421524736917254!51561$GO:0000074!regulation of progression through cell cycle!0.0438597620073579!322$GO:0051726!regulation of cell cycle!0.0438597620073579!322$GO:0022403!cell cycle phase!0.044310832096655!322$GO:0031324!negative regulation of cellular metabolic process!0.0449813148471854!322$GO:0051246!regulation of protein metabolic process!0.0482182281231848!322$GO:0009611!response to wounding!0.0482182281231848!51561$GO:0008134!transcription factor binding!0.0482182281231848!322$GO:0009892!negative regulation of metabolic process!0.0482182281231848!322
|gostat_on_coexpression_clusters=GO:0050760!negative regulation of thymidylate synthase biosynthetic process!0.00237450449389693!322$GO:0050758!regulation of thymidylate synthase biosynthetic process!0.00237450449389693!322$GO:0050757!thymidylate synthase biosynthetic process!0.00237450449389693!322$GO:0045749!negative regulation of S phase of mitotic cell cycle!0.0123009907713758!322$GO:0001540!beta-amyloid binding!0.0123009907713758!322$GO:0007090!regulation of S phase of mitotic cell cycle!0.0123009907713758!322$GO:0045930!negative regulation of progression through mitotic cell cycle!0.0123009907713758!322$GO:0033261!regulation of progression through S phase!0.0123009907713758!322$GO:0000084!S phase of mitotic cell cycle!0.0123009907713758!322$GO:0030426!growth cone!0.0123009907713758!322$GO:0030427!site of polarized growth!0.0123009907713758!322$GO:0051320!S phase!0.0124624789486762!322$GO:0007346!regulation of progression through mitotic cell cycle!0.0175268017854181!322$GO:0030027!lamellipodium!0.0194594735801954!322$GO:0017148!negative regulation of translation!0.0194594735801954!322$GO:0031327!negative regulation of cellular biosynthetic process!0.0200219068535414!322$GO:0009890!negative regulation of biosynthetic process!0.0202299818924186!322$GO:0030308!negative regulation of cell growth!0.0202299818924186!322$GO:0045792!negative regulation of cell size!0.0202299818924186!322$GO:0045926!negative regulation of growth!0.0217075291219072!322$GO:0031252!leading edge!0.0243979520439284!322$GO:0051329!interphase of mitotic cell cycle!0.0274886381140926!322$GO:0051325!interphase!0.0275265936430817!322$GO:0009615!response to virus!0.0275265936430817!51561$GO:0007050!cell cycle arrest!0.0275265936430817!322$GO:0051248!negative regulation of protein metabolic process!0.0275265936430817!322$GO:0048771!tissue remodeling!0.0275265936430817!51561$GO:0007409!axonogenesis!0.0275265936430817!322$GO:0045087!innate immune response!0.0275265936430817!51561$GO:0048667!neuron morphogenesis during differentiation!0.0275265936430817!322$GO:0048812!neurite morphogenesis!0.0275265936430817!322$GO:0000904!cellular morphogenesis during differentiation!0.0279972299614313!322$GO:0031175!neurite development!0.0290841708536053!322$GO:0048666!neuron development!0.0321926668132127!322$GO:0001558!regulation of cell growth!0.0327848518702859!322$GO:0006417!regulation of translation!0.0327848518702859!322$GO:0031326!regulation of cellular biosynthetic process!0.0327848518702859!322$GO:0016049!cell growth!0.0327848518702859!322$GO:0040008!regulation of growth!0.0327848518702859!322$GO:0032990!cell part morphogenesis!0.0327848518702859!322$GO:0030030!cell projection organization and biogenesis!0.0327848518702859!322$GO:0048858!cell projection morphogenesis!0.0327848518702859!322$GO:0008361!regulation of cell size!0.0327848518702859!322$GO:0051707!response to other organism!0.0327848518702859!51561$GO:0030182!neuron differentiation!0.0327848518702859!322$GO:0032501!multicellular organismal process!0.0327848518702859!322;51561$GO:0009889!regulation of biosynthetic process!0.0327848518702859!322$GO:0045786!negative regulation of progression through cell cycle!0.0332813801169429!322$GO:0048699!generation of neurons!0.0350566403475582!322$GO:0022008!neurogenesis!0.0371838177210064!322$GO:0009607!response to biotic stimulus!0.0396941228186807!51561$GO:0006954!inflammatory response!0.0396941228186807!51561$GO:0005125!cytokine activity!0.0411003848729342!51561$GO:0042995!cell projection!0.0411003848729342!322$GO:0000278!mitotic cell cycle!0.0420210337736801!322$GO:0051704!multi-organism process!0.0421524736917254!51561$GO:0000074!regulation of progression through cell cycle!0.0438597620073579!322$GO:0051726!regulation of cell cycle!0.0438597620073579!322$GO:0022403!cell cycle phase!0.044310832096655!322$GO:0031324!negative regulation of cellular metabolic process!0.0449813148471854!322$GO:0051246!regulation of protein metabolic process!0.0482182281231848!322$GO:0009611!response to wounding!0.0482182281231848!51561$GO:0008134!transcription factor binding!0.0482182281231848!322$GO:0009892!negative regulation of metabolic process!0.0482182281231848!322
|id=C3185
|id=C3185
|ontology_enrichment_celltype=CL:0000542!1.27e-29!53;CL:0000051!1.27e-29!53;CL:0000838!8.21e-29!52;CL:0000084!4.09e-27!25;CL:0000827!4.09e-27!25;CL:0000791!1.38e-20!18;CL:0000789!1.38e-20!18;CL:0002420!1.38e-20!18;CL:0002419!1.38e-20!18;CL:0000790!1.38e-20!18;CL:0002087!1.28e-14!119;CL:0000988!1.66e-14!182;CL:0000738!1.83e-13!140;CL:0000625!4.81e-13!11;CL:0000037!5.02e-13!172;CL:0000566!5.02e-13!172;CL:0002032!4.50e-11!165;CL:0000837!4.50e-11!165;CL:0002031!8.00e-11!124;CL:0000624!3.97e-08!6
|ontology_enrichment_celltype=CL:0000084!9.89e-46!25;CL:0000827!9.89e-46!25;CL:0000542!1.57e-40!53;CL:0000051!1.57e-40!53;CL:0000791!7.67e-39!18;CL:0000789!7.67e-39!18;CL:0002420!7.67e-39!18;CL:0002419!7.67e-39!18;CL:0000790!7.67e-39!18;CL:0000838!7.69e-39!52;CL:0002242!1.03e-38!55;CL:0000625!2.53e-22!11;CL:0002087!9.18e-20!115;CL:0000738!1.20e-18!136;CL:0000624!3.87e-16!6;CL:0000037!6.27e-15!168;CL:0000566!6.27e-15!168;CL:0000988!1.67e-14!177;CL:0002031!7.89e-14!120;CL:0002032!4.77e-12!161;CL:0000837!4.77e-12!161;CL:0000898!9.29e-09!3;CL:0000226!2.92e-08!3;CL:0000842!2.92e-08!3;CL:0000623!9.23e-08!3;CL:0000825!9.23e-08!3
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000178!2.93e-12!15;UBERON:0000179!2.93e-12!15;UBERON:0000463!2.93e-12!15
|ontology_enrichment_uberon=UBERON:0000178!1.11e-14!15;UBERON:0000179!1.11e-14!15;UBERON:0000463!1.11e-14!15;UBERON:0004177!1.36e-12!7;UBERON:0005057!1.36e-12!7;UBERON:0002370!4.18e-11!4;UBERON:0005058!4.18e-11!4;UBERON:0009113!4.18e-11!4;UBERON:0003295!4.18e-11!4;UBERON:0005562!4.18e-11!4;UBERON:0009722!1.22e-07!11;UBERON:0007690!1.22e-07!11;UBERON:0003351!2.26e-07!6
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}}
}}

Revision as of 14:52, 19 October 2012


Full id: C3185_chronic_acute_thymus_CD4_Hodgkin_CD8_NK



Phase1 CAGE Peaks

Hg19::chr11:6424016..6424033,-p7@APBB1
Hg19::chr4:108969174..108969197,-p@chr4:108969174..108969197
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Hg19::chr7:142498763..142498785,+p3@AJ568018


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:0050760negative regulation of thymidylate synthase biosynthetic process0.00237450449389693
GO:0050758regulation of thymidylate synthase biosynthetic process0.00237450449389693
GO:0050757thymidylate synthase biosynthetic process0.00237450449389693
GO:0045749negative regulation of S phase of mitotic cell cycle0.0123009907713758
GO:0001540beta-amyloid binding0.0123009907713758
GO:0007090regulation of S phase of mitotic cell cycle0.0123009907713758
GO:0045930negative regulation of progression through mitotic cell cycle0.0123009907713758
GO:0033261regulation of progression through S phase0.0123009907713758
GO:0000084S phase of mitotic cell cycle0.0123009907713758
GO:0030426growth cone0.0123009907713758
GO:0030427site of polarized growth0.0123009907713758
GO:0051320S phase0.0124624789486762
GO:0007346regulation of progression through mitotic cell cycle0.0175268017854181
GO:0030027lamellipodium0.0194594735801954
GO:0017148negative regulation of translation0.0194594735801954
GO:0031327negative regulation of cellular biosynthetic process0.0200219068535414
GO:0009890negative regulation of biosynthetic process0.0202299818924186
GO:0030308negative regulation of cell growth0.0202299818924186
GO:0045792negative regulation of cell size0.0202299818924186
GO:0045926negative regulation of growth0.0217075291219072
GO:0031252leading edge0.0243979520439284
GO:0051329interphase of mitotic cell cycle0.0274886381140926
GO:0051325interphase0.0275265936430817
GO:0009615response to virus0.0275265936430817
GO:0007050cell cycle arrest0.0275265936430817
GO:0051248negative regulation of protein metabolic process0.0275265936430817
GO:0048771tissue remodeling0.0275265936430817
GO:0007409axonogenesis0.0275265936430817
GO:0045087innate immune response0.0275265936430817
GO:0048667neuron morphogenesis during differentiation0.0275265936430817
GO:0048812neurite morphogenesis0.0275265936430817
GO:0000904cellular morphogenesis during differentiation0.0279972299614313
GO:0031175neurite development0.0290841708536053
GO:0048666neuron development0.0321926668132127
GO:0001558regulation of cell growth0.0327848518702859
GO:0006417regulation of translation0.0327848518702859
GO:0031326regulation of cellular biosynthetic process0.0327848518702859
GO:0016049cell growth0.0327848518702859
GO:0040008regulation of growth0.0327848518702859
GO:0032990cell part morphogenesis0.0327848518702859
GO:0030030cell projection organization and biogenesis0.0327848518702859
GO:0048858cell projection morphogenesis0.0327848518702859
GO:0008361regulation of cell size0.0327848518702859
GO:0051707response to other organism0.0327848518702859
GO:0030182neuron differentiation0.0327848518702859
GO:0032501multicellular organismal process0.0327848518702859
GO:0009889regulation of biosynthetic process0.0327848518702859
GO:0045786negative regulation of progression through cell cycle0.0332813801169429
GO:0048699generation of neurons0.0350566403475582
GO:0022008neurogenesis0.0371838177210064
GO:0009607response to biotic stimulus0.0396941228186807
GO:0006954inflammatory response0.0396941228186807
GO:0005125cytokine activity0.0411003848729342
GO:0042995cell projection0.0411003848729342
GO:0000278mitotic cell cycle0.0420210337736801
GO:0051704multi-organism process0.0421524736917254
GO:0000074regulation of progression through cell cycle0.0438597620073579
GO:0051726regulation of cell cycle0.0438597620073579
GO:0022403cell cycle phase0.044310832096655
GO:0031324negative regulation of cellular metabolic process0.0449813148471854
GO:0051246regulation of protein metabolic process0.0482182281231848
GO:0009611response to wounding0.0482182281231848
GO:0008134transcription factor binding0.0482182281231848
GO:0009892negative regulation of metabolic process0.0482182281231848



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
T cell9.89e-4625
pro-T cell9.89e-4625
lymphocyte1.57e-4053
common lymphoid progenitor1.57e-4053
mature alpha-beta T cell7.67e-3918
alpha-beta T cell7.67e-3918
immature T cell7.67e-3918
mature T cell7.67e-3918
immature alpha-beta T cell7.67e-3918
lymphoid lineage restricted progenitor cell7.69e-3952
nucleate cell1.03e-3855
CD8-positive, alpha-beta T cell2.53e-2211
nongranular leukocyte9.18e-20115
leukocyte1.20e-18136
CD4-positive, alpha-beta T cell3.87e-166
hematopoietic stem cell6.27e-15168
angioblastic mesenchymal cell6.27e-15168
hematopoietic cell1.67e-14177
hematopoietic lineage restricted progenitor cell7.89e-14120
hematopoietic oligopotent progenitor cell4.77e-12161
hematopoietic multipotent progenitor cell4.77e-12161
naive T cell9.29e-093
single nucleate cell2.92e-083
mononuclear cell2.92e-083
natural killer cell9.23e-083
pro-NK cell9.23e-083
Uber Anatomy
Ontology termp-valuen
blood1.11e-1415
haemolymphatic fluid1.11e-1415
organism substance1.11e-1415
hemopoietic organ1.36e-127
immune organ1.36e-127
thymus4.18e-114
hemolymphoid system gland4.18e-114
thymic region4.18e-114
pharyngeal gland4.18e-114
thymus primordium4.18e-114
entire pharyngeal arch endoderm1.22e-0711
early pharyngeal endoderm1.22e-0711
pharyngeal epithelium2.26e-076


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)

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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


This analysis result is provided for C0 - C305 clusters.