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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:33, 17 September 2013


Full id: C921_chronic_thymus_CD4_acute_CD8_Hodgkin_Peripheral



Phase1 CAGE Peaks

Hg19::chr17:80085772..80085810,-p@chr17:80085772..80085810
-
Hg19::chr2:128399902..128399934,-p11@LIMS2
Hg19::chr4:108991916..108991933,-p36@LEF1
Hg19::chr4:109086281..109086319,-p9@LEF1
Hg19::chr4:109087872..109087881,-p28@LEF1
Hg19::chr4:109088772..109088783,-p40@LEF1
Hg19::chr4:109088814..109088831,-p18@LEF1
Hg19::chr4:109088863..109088887,-p24@LEF1
Hg19::chr4:109089515..109089523,-p31@LEF1


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:0021542dentate gyrus development0.00812350064703412
GO:0021766hippocampus development0.00812350064703412
GO:0048341paraxial mesoderm formation0.00812350064703412
GO:0048340paraxial mesoderm morphogenesis0.00812350064703412
GO:0048339paraxial mesoderm development0.00812350064703412
GO:0021543pallium development0.00812350064703412
GO:0021761limbic system development0.00812350064703412
GO:0045843negative regulation of striated muscle development0.00812350064703412
GO:0008301DNA bending activity0.00857341781035285
GO:0021537telencephalon development0.00857341781035285
GO:0016202regulation of striated muscle development0.00857341781035285
GO:0030879mammary gland development0.00857341781035285
GO:0001890placenta development0.00857341781035285
GO:0001707mesoderm formation0.00857341781035285
GO:0048332mesoderm morphogenesis0.00857341781035285
GO:0001704formation of primary germ layer0.00857341781035285
GO:0001756somitogenesis0.00857341781035285
GO:0042475odontogenesis of dentine-containing teeth0.00857341781035285
GO:0042476odontogenesis0.00953361626905974
GO:0007369gastrulation0.00953361626905974
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.00953361626905974
GO:0035282segmentation0.00953361626905974
GO:0030111regulation of Wnt receptor signaling pathway0.00953361626905974
GO:0030326embryonic limb morphogenesis0.0103600419735333
GO:0035113embryonic appendage morphogenesis0.0103600419735333
GO:0060173limb development0.0103600419735333
GO:0035107appendage morphogenesis0.0103600419735333
GO:0035108limb morphogenesis0.0103600419735333
GO:0048736appendage development0.0103600419735333
GO:0007498mesoderm development0.0116710002566134
GO:0030900forebrain development0.0116710002566134
GO:0048732gland development0.0116710002566134
GO:0009952anterior/posterior pattern formation0.0135298008372182
GO:0048729tissue morphogenesis0.0171865009779544
GO:0003002regionalization0.0197626731549567
GO:0014706striated muscle development0.0197626731549567
GO:0048598embryonic morphogenesis0.0197626731549567
GO:0009792embryonic development ending in birth or egg hatching0.0197626731549567
GO:0043009chordate embryonic development0.0197626731549567
GO:0003682chromatin binding0.0239255239947893
GO:0007389pattern specification process0.0245208906358903
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0245208906358903
GO:0007420brain development0.0256133909633335
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0256133909633335
GO:0016055Wnt receptor signaling pathway0.0261229374633611
GO:0048646anatomical structure formation0.0269617993721472
GO:0007517muscle development0.0296567886776082
GO:0045892negative regulation of transcription, DNA-dependent0.0342570240448924
GO:0005667transcription factor complex0.034711482782422
GO:0045893positive regulation of transcription, DNA-dependent0.0361161499760726
GO:0007417central nervous system development0.0365893036118252
GO:0009790embryonic development0.0365893036118252
GO:0003702RNA polymerase II transcription factor activity0.0418039915144584
GO:0045941positive regulation of transcription0.0418039915144584
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0420373414030184
GO:0016481negative regulation of transcription0.0420373414030184
GO:0009888tissue development0.0430868950323471
GO:0016563transcription activator activity0.0430868950323471
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0437209074162008
GO:0009887organ morphogenesis0.0483523964577336
GO:0031325positive regulation of cellular metabolic process0.0483523964577336
GO:0031324negative regulation of cellular metabolic process0.0496461326225933



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>

Uber Anatomy
Ontology termp-valuen
blood8.00e-0915
haemolymphatic fluid8.00e-0915
organism substance8.00e-0915
hemopoietic organ1.43e-087
immune organ1.43e-087


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)
MA0003.10.818094
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.11.50001
MA0017.10.815464
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.559235
MA0050.10.403421
MA0051.11.27173
MA0052.10.795605
MA0055.10.693769
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.851955
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.602377
MA0074.10.509711
MA0076.10.901394
MA0077.10.832987
MA0078.10.607575
MA0081.11.55973
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.854766
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.12.39359
MA0114.10.200901
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.177438
MA0146.10.175555
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.21.95022
MA0035.21.19307
MA0039.20.109483
MA0138.20.608783
MA0002.20.46405
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.225151
MA0155.10.0402662
MA0156.11.43134
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.502732
MA0163.11.18882
MA0164.10.583138
MA0080.21.35856
MA0018.20.556211
MA0099.20.481058
MA0079.20.48507
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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

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.

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