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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.173130417906961,-

Latest revision as of 12:35, 17 September 2013


Full id: C3904_CD14_Mast_CD19_Neutrophils_CD4_Eosinophils_CD8



Phase1 CAGE Peaks

Hg19::chr1:171454639..171454657,+p2@PRRC2C
Hg19::chr1:171454659..171454723,+p1@PRRC2C
Hg19::chr7:23571586..23571610,-p1@TRA2A


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:0000375RNA splicing, via transesterification reactions0.0185446838572942
GO:0000398nuclear mRNA splicing, via spliceosome0.0185446838572942
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0185446838572942
GO:0008380RNA splicing0.0413281525962557
GO:0006397mRNA processing0.0413281525962557
GO:0016071mRNA metabolic process0.0413281525962557
GO:0042802identical protein binding0.0413281525962557



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 cell2.13e-31168
angioblastic mesenchymal cell2.13e-31168
leukocyte2.62e-31136
hematopoietic oligopotent progenitor cell2.32e-29161
hematopoietic multipotent progenitor cell2.32e-29161
hematopoietic cell1.66e-28177
nongranular leukocyte2.07e-23115
hematopoietic lineage restricted progenitor cell6.01e-23120
myeloid cell9.35e-18108
common myeloid progenitor9.35e-18108
myeloid leukocyte2.96e-1672
classical monocyte4.07e-1542
CD14-positive, CD16-negative classical monocyte4.07e-1542
granulocyte monocyte progenitor cell6.72e-1467
macrophage dendritic cell progenitor4.67e-1261
defensive cell7.19e-1248
phagocyte7.19e-1248
myeloid lineage restricted progenitor cell7.82e-1266
monopoietic cell2.40e-1159
monocyte2.40e-1159
monoblast2.40e-1159
promonocyte2.40e-1159
lymphocyte5.09e-1153
common lymphoid progenitor5.09e-1153
lymphoid lineage restricted progenitor cell1.02e-1052
nucleate cell4.32e-1055
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.89e-1498
blood island2.89e-1498
hemolymphoid system1.26e-11108
bone element1.69e-1082
bone marrow3.32e-1076
immune system8.43e-0993
skeletal element5.39e-0890
skeletal system8.34e-07100
Disease
Ontology termp-valuen
cancer1.50e-08235
disease of cellular proliferation4.88e-08239
cell type cancer8.56e-07143


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)
MA0003.10.178364
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.11.70328
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.12.8848
MA0073.10.0834661
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.12.29531
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.12.32251
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
ATF3#467214.97544968400580.005768294540793880.0259580710766103
BHLHE40#8553229.91454236465160.001467483527106140.00939741934437664
BRCA1#672320.18423064322380.0001215704860271640.00164252263779961
CCNT2#90536.336201576962630.003930750035764890.0190127641249189
E2F1#186934.907389214879320.008460985347239390.0325532086454351
E2F4#1874312.66806031528440.0004917987006298980.00437392186792864
E2F6#187635.017155731697390.00791769806886330.0322409727313636
FOSL2#2355211.28680040304110.0100534586973120.0376780124480053
GATA3#2625218.15767757147070.003944546819279620.0189522254799993
GTF2B#2959331.94382993432423.06634405746243e-050.000627933151014351
GTF2F1#2962312.73966087675770.0004835525047438590.00434087502517998
HMGN3#932438.178547723350590.001827766942164210.0108763119863648
IRF4#3662214.60967512449610.006056122473217890.0268393182967158
MAX#414936.452555509007120.003721913834265510.0186638958533085
MYC#460935.22228187160940.007020843755740150.0294667216285865
NANOG#79923219.49651898734180.003427255648501020.0174485304023495
NFE2#4778251.4695071010860.0004987653528392110.00440661151215417
NFKB1#479035.488063424193840.006049381815655430.0269742715158927
POU2F2#545239.106124057742520.001324165192682130.00882655658402661
PRDM1#639287.88730385164050.0001716248848029080.00209176465677803
RFX5#5993312.04791082719510.0005717246050312580.00484819308418801
SIRT6#515482102.4256026600170.0001264379392731220.0016828153357647
SMARCC1#6599229.10890621308760.001549200814224140.00984286311210334
SMARCC2#6601262.77024961793170.0003358375417085070.00341757156956979
SMC3#9126210.02995522995520.0126656379767470.0457521639683689
SP1#666735.69838137814090.005403962701712170.0246671529984317
STAT1#6772213.80439166479950.006770931708444080.0287529209033988
TAF7#6879311.43306940492390.0006690181981945830.00543324973571105
TAL1#6886219.91241111829350.003287176608740550.0170140468748267
TRIM28#10155318.59052504526250.0001555969297255280.00197117755259636
USF1#739136.361499277207960.00388404057290560.0190390178068942
YY1#752834.911170749853860.008441455341808260.0329601149410465



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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