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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 12:10, 17 September 2013


Full id: C2643_Eosinophils_acute_Neutrophils_CD14_Whole_Monocytederived_Macrophage



Phase1 CAGE Peaks

Hg19::chr22:37257002..37257013,+p4@NCF4
Hg19::chr22:37257015..37257065,+p1@NCF4
Hg19::chr22:37257072..37257091,+p2@NCF4
Hg19::chr22:37257098..37257115,+p3@NCF4


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

No GOStat results

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 cell2.18e-78168
angioblastic mesenchymal cell2.18e-78168
hematopoietic oligopotent progenitor cell5.17e-75161
hematopoietic multipotent progenitor cell5.17e-75161
hematopoietic cell1.10e-74177
myeloid cell2.53e-65108
common myeloid progenitor2.53e-65108
leukocyte5.27e-61136
hematopoietic lineage restricted progenitor cell6.72e-51120
myeloid leukocyte5.23e-4872
nongranular leukocyte1.50e-47115
granulocyte monocyte progenitor cell1.22e-4367
myeloid lineage restricted progenitor cell5.91e-4266
macrophage dendritic cell progenitor2.67e-4061
monopoietic cell9.28e-3959
monocyte9.28e-3959
monoblast9.28e-3959
promonocyte9.28e-3959
defensive cell2.54e-3448
phagocyte2.54e-3448
classical monocyte1.17e-2942
CD14-positive, CD16-negative classical monocyte1.17e-2942
nucleate cell6.32e-1155
stuff accumulating cell6.80e-1187
mesenchymal cell7.36e-11354
lymphocyte2.37e-1053
common lymphoid progenitor2.37e-1053
lymphocyte of B lineage2.49e-1024
pro-B cell2.49e-1024
lymphoid lineage restricted progenitor cell3.98e-1052
connective tissue cell7.67e-10361
dendritic cell1.04e-0710
granulocyte1.10e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.46e-5098
blood island1.46e-5098
hemolymphoid system6.98e-45108
bone marrow1.12e-3776
immune system6.54e-3593
bone element1.10e-3282
skeletal element3.75e-2790
adult organism1.03e-26114
skeletal system3.13e-22100
lateral plate mesoderm2.42e-13203
blood9.08e-1115
haemolymphatic fluid9.08e-1115
organism substance9.08e-1115
connective tissue7.73e-09371
musculoskeletal system5.44e-07167
Disease
Ontology termp-valuen
hematologic cancer6.34e-1551
immune system cancer6.34e-1551
leukemia2.31e-1439
myeloid leukemia2.93e-1431


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)
MA0003.10.233555
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.13.06856
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.12.66951
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.12.9994
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.14.62806
MA0139.10.344952
MA0140.10.779643
MA0141.13.64588
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.11.75643
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.22.63392
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.12.36058
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.12.98688
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.29.8636
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BCL11A#53335428.36945510360711.542446414682e-065.8964700257311e-05
BCL3#602434.54710280373837.01262157705428e-073.15142506405324e-05
EBF1#187948.9064668465690.00015887907472010.0019977331669507
EGR1#195844.988179094810140.001615011500076050.0101529035126975
ELF1#199744.258097958807540.003041525565781240.0161057591930551
IRF4#3662421.91451268674414.33289161192893e-060.000136548843409247
NFKB1#479045.488063424193840.001102199566301980.0076844205944601
PAX5#507946.669565531177830.0005052774169483260.00444309742768933
REST#597849.650028716128020.0001152825614219170.00157262218290799
SP1#666745.69838137814090.0009482606065333980.00684844682150208
SPI1#668848.204323508522730.000220661881527680.00249601497290906
SRF#6722413.79717826216782.75840773062708e-050.000584944862901444
TCF12#6938410.63446490218647.8163066689251e-050.00120136460955978
YY1#752844.911170749853860.00171871838055440.0106941453051368
ZEB1#6935416.88843201754391.22862303393937e-050.000304499670245833



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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