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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0.

Latest revision as of 11:43, 17 September 2013


Full id: C1347_testis_Neutrophils_Eosinophils_CD14_Basophils_blood_Whole



Phase1 CAGE Peaks

Hg19::chr11:64545206..64545220,-p18@SF1
Hg19::chr11:64545222..64545241,-p14@SF1
Hg19::chr1:21503755..21503801,-p6@EIF4G3
Hg19::chr1:33430424..33430450,-p3@RNF19B
Hg19::chr22:40440137..40440179,-p2@BC038752
Hg19::chr2:176867534..176867553,-p3@KIAA1715


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:0022618protein-RNA complex assembly0.010613566923
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0157454819616763
GO:0048662negative regulation of smooth muscle cell proliferation0.0157454819616763
GO:0000389nuclear mRNA 3'-splice site recognition0.0157454819616763
GO:0000339RNA cap binding0.0176333824446613
GO:0016281eukaryotic translation initiation factor 4F complex0.0195865918599737
GO:0048660regulation of smooth muscle cell proliferation0.0195865918599737
GO:0006376mRNA splice site selection0.0195865918599737
GO:0048659smooth muscle cell proliferation0.0195865918599737
GO:0033002muscle cell proliferation0.0251760894769034
GO:0065003macromolecular complex assembly0.0280184993791957
GO:0022607cellular component assembly0.0290365082605116
GO:0000245spliceosome assembly0.0290365082605116
GO:0003723RNA binding0.0351989918807554
GO:0005515protein binding0.0351989918807554
GO:0006446regulation of translational initiation0.0439881637215268
GO:0000375RNA splicing, via transesterification reactions0.0462747063103437
GO:0000398nuclear mRNA splicing, via spliceosome0.0462747063103437
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0462747063103437



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
regional part of nervous system1.56e-1653
regional part of brain1.56e-1653
neural tube2.29e-1656
neural rod2.29e-1656
future spinal cord2.29e-1656
neural keel2.29e-1656
central nervous system4.04e-1581
brain1.61e-1468
future brain1.61e-1468
regional part of forebrain4.66e-1341
forebrain4.66e-1341
anterior neural tube4.66e-1341
future forebrain4.66e-1341
hematopoietic system2.03e-1298
blood island2.03e-1298
adult organism3.86e-12114
hemolymphoid system1.13e-11108
nervous system1.30e-1189
brain grey matter1.42e-1134
gray matter1.42e-1134
telencephalon1.94e-1134
neocortex5.66e-1120
cerebral hemisphere7.30e-1132
regional part of cerebral cortex1.68e-1022
regional part of telencephalon1.94e-1032
cerebral cortex4.90e-1025
pallium4.90e-1025
neural plate6.83e-1082
presumptive neural plate6.83e-1082
blood7.54e-0915
haemolymphatic fluid7.54e-0915
organism substance7.54e-0915
neurectoderm1.13e-0886
pre-chordal neural plate2.00e-0861
bone marrow5.78e-0776
immune system9.53e-0793
bone element9.93e-0782


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)
MA0003.11.37104
MA0004.10.558729
MA0006.11.79433
MA0007.10.539222
MA0009.11.03681
MA0014.10.788761
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.347876
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.830067
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.11.55935
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.11.8938
MA0147.12.3862
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0929059
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.22.90014
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.62382
MA0102.21.58513
MA0258.10.289793
MA0259.11.6038
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
NRF1#489936.105139723855450.009090162079396740.034401110171762
POLR2A#543062.147453176558070.01019570676818780.0379970532102043
SIN3A#2594243.605923151210090.01273893844487140.0459375040481983



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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