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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0277951421569895,

Latest revision as of 11:50, 17 September 2013


Full id: C1725_Neutrophils_Eosinophils_Mast_CD8_Natural_CD4_cord



Phase1 CAGE Peaks

Hg19::chr14:45431091..45431175,-p1@KLHL28
Hg19::chr3:39093481..39093520,+p1@WDR48
Hg19::chr4:4291944..4292011,+p1@ZBTB49
Hg19::chr6:42750549..42750592,-p@chr6:42750549..42750592
-
Hg19::chr9:32550839..32550962,-p3@TOPORS


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:0017033DNA topoisomerase I binding0.0054750971388202
GO:0051457maintenance of protein localization in nucleus0.0136861311971243
GO:0032507maintenance of cellular protein localization0.0284495579902943
GO:0051651maintenance of cellular localization0.0284495579902943
GO:0045185maintenance of protein localization0.0284495579902943
GO:0051235maintenance of localization0.0373691275791586



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
leukocyte2.95e-33136
hematopoietic stem cell5.29e-28168
angioblastic mesenchymal cell5.29e-28168
hematopoietic cell6.34e-26177
hematopoietic lineage restricted progenitor cell2.39e-25120
hematopoietic oligopotent progenitor cell7.85e-25161
hematopoietic multipotent progenitor cell7.85e-25161
nongranular leukocyte1.67e-23115
nucleate cell8.45e-1555
lymphoid lineage restricted progenitor cell2.15e-1452
myeloid leukocyte2.31e-1472
lymphocyte2.85e-1453
common lymphoid progenitor2.85e-1453
classical monocyte3.53e-1442
CD14-positive, CD16-negative classical monocyte3.53e-1442
myeloid cell1.97e-11108
common myeloid progenitor1.97e-11108
defensive cell5.21e-1148
phagocyte5.21e-1148
myeloid lineage restricted progenitor cell6.38e-1166
mature alpha-beta T cell6.59e-1118
alpha-beta T cell6.59e-1118
immature T cell6.59e-1118
mature T cell6.59e-1118
immature alpha-beta T cell6.59e-1118
granulocyte monocyte progenitor cell7.78e-1167
T cell1.55e-0925
pro-T cell1.55e-0925
macrophage dendritic cell progenitor3.09e-0961
monopoietic cell1.06e-0859
monocyte1.06e-0859
monoblast1.06e-0859
promonocyte1.06e-0859
CD8-positive, alpha-beta T cell7.62e-0811
B cell9.99e-0714
Uber Anatomy
Ontology termp-valuen
adult organism3.45e-21114
central nervous system9.72e-1781
neural tube1.40e-1656
neural rod1.40e-1656
future spinal cord1.40e-1656
neural keel1.40e-1656
nervous system6.74e-1689
hematopoietic system8.88e-1698
blood island8.88e-1698
regional part of nervous system9.67e-1653
regional part of brain9.67e-1653
regional part of forebrain1.58e-1441
forebrain1.58e-1441
anterior neural tube1.58e-1441
future forebrain1.58e-1441
brain1.40e-1368
future brain1.40e-1368
hemolymphoid system2.43e-13108
telencephalon2.80e-1234
brain grey matter4.55e-1234
gray matter4.55e-1234
cerebral hemisphere1.17e-1132
regional part of telencephalon1.48e-1132
regional part of cerebral cortex1.65e-0922
cerebral cortex3.67e-0925
pallium3.67e-0925
bone marrow4.64e-0976
neocortex7.83e-0920
bone element1.52e-0882
immune system1.81e-0893
neurectoderm2.04e-0886
neural plate5.72e-0882
presumptive neural plate5.72e-0882
blood7.27e-0815
haemolymphatic fluid7.27e-0815
organism substance7.27e-0815
skeletal element1.97e-0790


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)
MA0003.10.737422
MA0004.11.51734
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.11.18667
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.5062
MA0056.10
MA0057.12.36624
MA0058.11.29981
MA0059.12.23433
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.12.7757
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.551452
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.12.01552
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.868598
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.22.17426
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.425004
MA0065.22.03954
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.469165
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.23.94612
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CHD2#110636.206413700470110.007774550126275590.0319520793577088
E2F1#186954.907389214879320.0003512818099256460.00352561223782669
HEY1#2346254.040111043105710.0009288852205177990.00674021007056614
HNF4G#3174211.50136901057870.01127438304921050.0413747950130536
NANOG#79923211.69791139240510.01091164951956080.0402174535634321
NFKB1#479044.390450739355070.004707732692524960.0222023434036854
NR2C2#7182319.56876654314450.0002750171700966610.00293057016913837
SIN3A#2594244.327107781452110.004977052855762880.0232405626040874
SP2#6668210.46141219753790.01353191183347140.0477775300870831
TAF1#687253.343046285745290.002394600090870310.0135278649261862
TBP#690853.706770687096390.001428755106721120.00918376136083501
YY1#752843.928936599883080.007193866269917620.0298379745577413



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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