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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.338474986694436,0.290068703032943,0.302073425901529,0,0,0,0.062557317541557,0,0.492004430513704,0.237561678138751,0.299432350369393,0.295252180953235,0,0.169377132044987,0.180455955570557,0.108084917820001,0.139210117864267,0.0943257785523457,0.128278735573994,0.20510354328982,0,0,0.0990452042849908,0,0.227755975528437,0.068189673650693,0,0.219106453218697,0.224461115623354,0.155918859323999,0.31505294665293,0.325757653039325,0,0,0.0394935469382982,0,0.110660147363526,0.097587874238361,0,0.0486718136065485,0,0.0783317607528795,0.205583124092593,0.239688610815101,0.059704227710324,0,0,0,0,0,0,0,0,0,0.440903172569491,0.370981235885067,0.504191624525997,0.211162591594548,0.342657128871699,0.383793280947914,0.293130182798069,0.463610457803615,0.515456810409039,0.616692759714401,0.324798940647361,0.419050068912485,0.433625888312579,0.367338449346846,0.867861732630121,0.794392375431382,0.737324813402233,0.859165806345739,0.752729195633015,0.736531393867099,0.815863402547789,0.637148668129885,0.417669093727704,0.275572907280555,0.288495509957726,0.699123972436227,0.54656710025896,0.772294915521897,0.75684369741379,0.736547811965195,1.05163683894404,1.04929347192214,1.01517394826122,0.72474719385036,0.607204383717324,0.523137833522213,0.576887758051652,0.798964963078299,0.69656668169626,0.585613679514811,0.860213108773882,0.717444360745542,0.564683589578547,0.733499062076616,0.681725066997356,0.664800819857773,0.514615364999664,0.836535095884382,0,0,0,0,0,0,0,0,0,0,0.0329502515212901,0.133474480407003,0,0,0,0,0,0.270145155325134,0.331222719243351,0.318373817060259,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0780802955402416,0.0238698307237727,0.0428357178336246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.27483329820609,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0575805665668305,0,0,0,0,0.0222883133077808,0.0946494374619137,0,0.0595083336059311,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.326510248395875,0.65058135784851,0.671976131484004,0.635463017165985,0,0,0,0.0336314698420933,0,0.242791553592671,0,0.262173581098575,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.650415125665505,0.675399375440246,0.610932890974173,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0594199276895958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0195372020314829,0,0,0,0,0.392832528358756,0.460353946638454,0.33027054911511,0.636356907487515,0.586003173237263,0.469147221647532,0.499704364577129,0.412670562882006,0,0,0,0,0,0.697528837682505,0.3733266069702,0.467660220598499,0.460865103613587,0.162211412698315,0.256301254125474,0.368745804840252,0.757980268141155,0.083664529874431,0.272427308522646,0.215541148780788,0.0323390519651663,0.29403398776618,0.426451708934959,0.0641196992451515,0.773707697365373,0.79562412320227,0.726294322834175,0.256512761267504,0,0,0,0.513780184762955,0,0,0,0,0,0,0,0,0,0,0.0824118928404978,0.0229173581225888,0.158243004065645,0,0.112285109921075,0.323280088491714,0.0487904998923745,0,0,0,0,0,0.937373359119162,0.107489843572136,0.762653198909275,0,0.294319102417383,0.19140680383259,0.238280904943946,0,0,0,0,0,0,0.178197101007194,0,0,0,0,0,0,0,0.127967493649321,0,0,0,0,0,0,0,0,0,0,0.152883378286132,0.340178052266368,0.0333886937094506,0,0,0,0,0,0,0,0,0,0,0.0768960488038005,0.207103666835013,0.056389799308811,0.0505977919678937,0.0431350293094685,0.0141638297223524,0,0,0.189592591802658,0,0.0471971940941162,0.144444803709627,0.172187014549508,0.256015583791751,0.0266094859650764,0.00989962032630095,0,0,0,0,0,0,0,0,0,0,0.091518129972546,0,0,0,0,0.0207965764275319,0,0,0,0.0393578995913525,0.194426117202795,0,0.0645768949458293,0.119209159374346,0,0,0,0.098457478620693,0,0,0,0,0,0,0,0,0,0.668431389036333,0,0.176946455160923,0,0,0,0,0,0,0.0141195453442412,0,0,0,0,0,0,0,0,0.102123460698321,0.0647398703344467,0.127780940537644,0,0,0,0.210588868390646,0,0,0.0111016828724432,0,0,0,0,0,0,0,0,0,0,0.0660220147767975,0,0,0,0,0,0.0269678279474476,0,0,0.084066558699748,0.0317050203334407,0,0.696297678505703,0,0.128779974837085,0,0,0,0,0,0,0,0.281992956912365,0.181757994944978,0,0,0.0261639379934246,0.028137645546619,0,0,0,0,0.587821226566095,0.405633244142288,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.106026559445686,0,0,0,0,0,0,0.618751151344952,0.39634226200899,0,0,0,0,0,0.331602251107742,0.21223653258897,0,0.0787039861614065,0,0,0,0,0,0.690610291193911,0.0957620213067515,0,0,0.215118051257175,0,0.192197555150607,0.404200630304271,0.393270033267688,0.21922632414764,0.255308805568518,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.232694033256932,0.217824315280836,0.115925766787729,0.184931743410171,0.255224734859015,0,0,0,0,0,0,0,0.0445394404812913,0,0.088157441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|full_id=C712_thymus_biphenotypic_CD4_non_granulocyte_merkel_acute
|full_id=C712_thymus_biphenotypic_CD4_non_granulocyte_merkel_acute
|gostat_on_coexpression_clusters=GO:0004115!3',5'-cyclic-AMP phosphodiesterase activity!0.0284167707669588!5150$GO:0016571!histone methylation!0.0284167707669588!6304$GO:0005720!nuclear heterochromatin!0.0284167707669588!6304$GO:0000792!heterochromatin!0.0284167707669588!6304$GO:0008213!protein amino acid alkylation!0.0284167707669588!6304$GO:0006479!protein amino acid methylation!0.0284167707669588!6304$GO:0000790!nuclear chromatin!0.0284167707669588!6304$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase activity!0.0360071200977271!5150$GO:0043414!biopolymer methylation!0.0360071200977271!6304$GO:0004112!cyclic-nucleotide phosphodiesterase activity!0.0360071200977271!5150$GO:0016570!histone modification!0.0360071200977271!6304$GO:0016569!covalent chromatin modification!0.0360071200977271!6304$GO:0044454!nuclear chromosome part!0.0444142842183568!6304$GO:0032259!methylation!0.0444142842183568!6304
|gostat_on_coexpression_clusters=GO:0004115!3',5'-cyclic-AMP phosphodiesterase activity!0.0284167707669588!5150$GO:0016571!histone methylation!0.0284167707669588!6304$GO:0005720!nuclear heterochromatin!0.0284167707669588!6304$GO:0000792!heterochromatin!0.0284167707669588!6304$GO:0008213!protein amino acid alkylation!0.0284167707669588!6304$GO:0006479!protein amino acid methylation!0.0284167707669588!6304$GO:0000790!nuclear chromatin!0.0284167707669588!6304$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase activity!0.0360071200977271!5150$GO:0043414!biopolymer methylation!0.0360071200977271!6304$GO:0004112!cyclic-nucleotide phosphodiesterase activity!0.0360071200977271!5150$GO:0016570!histone modification!0.0360071200977271!6304$GO:0016569!covalent chromatin modification!0.0360071200977271!6304$GO:0044454!nuclear chromosome part!0.0444142842183568!6304$GO:0032259!methylation!0.0444142842183568!6304

Revision as of 18:24, 12 September 2012


Full id: C712_thymus_biphenotypic_CD4_non_granulocyte_merkel_acute



Phase1 CAGE Peaks

Hg19::chr3:18480105..18480108,-p48@SATB1
Hg19::chr3:18480151..18480162,-p18@SATB1
Hg19::chr3:18480173..18480189,-p6@SATB1
Hg19::chr3:18486202..18486209,-p5@TBC1D5
Hg19::chr3:18486296..18486319,-p3@TBC1D5
Hg19::chr3:18486324..18486338,-p4@TBC1D5
Hg19::chr3:18486354..18486377,-p2@SATB1
Hg19::chr3:18486459..18486481,+p2@ENST00000414198
Hg19::chr3:18486486..18486500,+p1@ENST00000414198
Hg19::chr3:18487033..18487044,-p23@SATB1
Hg19::chr3:18487057..18487105,-p4@SATB1
Hg19::chr8:66754259..66754276,-p2@PDE7A


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:00041153',5'-cyclic-AMP phosphodiesterase activity0.0284167707669588
GO:0016571histone methylation0.0284167707669588
GO:0005720nuclear heterochromatin0.0284167707669588
GO:0000792heterochromatin0.0284167707669588
GO:0008213protein amino acid alkylation0.0284167707669588
GO:0006479protein amino acid methylation0.0284167707669588
GO:0000790nuclear chromatin0.0284167707669588
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0360071200977271
GO:0043414biopolymer methylation0.0360071200977271
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0360071200977271
GO:0016570histone modification0.0360071200977271
GO:0016569covalent chromatin modification0.0360071200977271
GO:0044454nuclear chromosome part0.0444142842183568
GO:0032259methylation0.0444142842183568



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 cell2.96e-42172
angioblastic mesenchymal cell2.96e-42172
hematopoietic cell1.61e-38182
hematopoietic oligopotent progenitor cell1.90e-38165
hematopoietic multipotent progenitor cell1.90e-38165
leukocyte2.25e-34140
nongranular leukocyte7.02e-30119
hematopoietic lineage restricted progenitor cell1.13e-28124
lymphoid lineage restricted progenitor cell5.75e-2052
lymphocyte1.01e-1953
common lymphoid progenitor1.01e-1953
myeloid cell1.64e-18112
common myeloid progenitor1.64e-18112
T cell1.68e-1425
pro-T cell1.68e-1425
myeloid leukocyte1.89e-1376
mature alpha-beta T cell5.54e-1218
alpha-beta T cell5.54e-1218
immature T cell5.54e-1218
mature T cell5.54e-1218
immature alpha-beta T cell5.54e-1218
granulocyte monocyte progenitor cell3.32e-1171
myeloid lineage restricted progenitor cell1.92e-1070
monopoietic cell7.37e-1063
monocyte7.37e-1063
monoblast7.37e-1063
promonocyte7.37e-1063
macrophage dendritic cell progenitor8.99e-1065
CD14-positive, CD16-negative classical monocyte9.42e-0942
classical monocyte4.46e-0845
CD8-positive, alpha-beta T cell5.03e-0811
B cell3.60e-0714
Uber Anatomy
Ontology termp-valuen
adult organism5.91e-17115
hematopoietic system1.87e-15102
blood island1.87e-15102
hemolymphoid system4.49e-12112
neural tube1.30e-0857
neural rod1.30e-0857
future spinal cord1.30e-0857
neural keel1.30e-0857
anterior neural tube1.58e-0842
bone marrow1.63e-0880
regional part of forebrain1.90e-0841
forebrain1.90e-0841
future forebrain1.90e-0841
regional part of cerebral cortex2.23e-0822
telencephalon2.41e-0834
cerebral hemisphere2.80e-0832
gray matter3.41e-0834
brain grey matter3.41e-0834
neocortex4.47e-0820
regional part of telencephalon4.96e-0833
regional part of nervous system6.54e-0894
nervous system6.54e-0894
central nervous system7.20e-0882
blood7.46e-0815
haemolymphatic fluid7.46e-0815
organism substance7.46e-0815
bone element8.69e-0886
cerebral cortex1.08e-0725
pallium1.08e-0725
Disease
Ontology termp-valuen
hematologic cancer1.41e-1051
immune system cancer1.41e-1051
leukemia3.49e-1039
myeloid leukemia2.01e-0831


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
CTCF#1066473.12681621762710.002570345138407310.0142199531682446



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.