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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 12:08, 17 September 2013


Full id: C2584_Dendritic_CD14_Basophils_CD14CD16_Peripheral_CD34_granulocyte



Phase1 CAGE Peaks

Hg19::chr1:42194773..42194782,+p@chr1:42194773..42194782
+
Hg19::chr22:44422556..44422575,-p@chr22:44422556..44422575
-
Hg19::chr2:128321442..128321453,+p@chr2:128321442..128321453
+
Hg19::chr8:11724934..11724951,+p@chr8:11724934..11724951
+


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><br>

Cell Type
Ontology termp-valuen
classical monocyte1.56e-8542
CD14-positive, CD16-negative classical monocyte1.56e-8542
defensive cell5.11e-7748
phagocyte5.11e-7748
macrophage dendritic cell progenitor1.04e-6661
granulocyte monocyte progenitor cell1.13e-6567
leukocyte5.84e-63136
monopoietic cell1.23e-6259
monocyte1.23e-6259
monoblast1.23e-6259
promonocyte1.23e-6259
myeloid leukocyte1.50e-6072
myeloid lineage restricted progenitor cell1.56e-5766
hematopoietic stem cell5.69e-57168
angioblastic mesenchymal cell5.69e-57168
nongranular leukocyte9.53e-57115
hematopoietic lineage restricted progenitor cell2.69e-53120
hematopoietic cell3.45e-53177
myeloid cell4.51e-48108
common myeloid progenitor4.51e-48108
hematopoietic oligopotent progenitor cell7.39e-48161
hematopoietic multipotent progenitor cell7.39e-48161
stuff accumulating cell5.32e-3787
intermediate monocyte1.63e-229
CD14-positive, CD16-positive monocyte1.63e-229
mesenchymal cell7.73e-18354
connective tissue cell3.72e-17361
motile cell9.32e-15386
stem cell5.83e-13441
multi fate stem cell1.78e-12427
somatic stem cell4.61e-12433
plasmacytoid dendritic cell3.42e-093
single nucleate cell1.36e-083
mononuclear cell1.36e-083
basophil1.92e-083
non-classical monocyte3.64e-083
CD14-low, CD16-positive monocyte3.64e-083
natural killer cell5.89e-083
pro-NK cell5.89e-083
Uber Anatomy
Ontology termp-valuen
bone marrow4.51e-5976
bone element8.24e-5482
immune system2.25e-5293
hematopoietic system4.28e-5298
blood island4.28e-5298
hemolymphoid system5.80e-50108
skeletal element7.03e-4890
skeletal system8.54e-42100
lateral plate mesoderm3.40e-22203
musculoskeletal system7.04e-20167
connective tissue3.17e-16371
mesoderm5.94e-10315
mesoderm-derived structure5.94e-10315
presumptive mesoderm5.94e-10315


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)
MA0003.10.443649
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.10.69331
MA0058.12.50688
MA0059.12.50216
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.11.15856
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
MA0136.10.832277
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.8309
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.12.08227
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
BATF#10538212.17890089615180.009566758805047810.0360220183451847
BCL11A#53335214.18472755180350.007108328585298740.0296267351392775
CHD2#110637.758017125587640.003351522464536340.0172999384507345
EBF1#187936.679850134926750.005184294118278910.0240512834674365
IRF4#3662210.95725634337210.01174530180688030.042848525059689
MEF2A#4205314.0574231822330.0005830038854186610.00488827414814061
MEF2C#4208220.6556772463120.003402570579445040.0173583953080627
PAX5#507935.002174148383370.01196533174786410.0435023074014891
SPI1#668836.153242631392040.006580387113059030.0281025986383469
TCF12#693837.975848676639820.003090920396013070.0162798242593781



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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