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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:44, 17 September 2013


Full id: C1411_immature_Dendritic_CD19_Mast_CD14_Neutrophils_CD34



Phase1 CAGE Peaks

Hg19::chr15:74677677..74677688,+p@chr15:74677677..74677688
+
Hg19::chr15:74677699..74677722,+p@chr15:74677699..74677722
+
Hg19::chr15:74689107..74689118,+p@chr15:74689107..74689118
+
Hg19::chr16:22218470..22218480,-p@chr16:22218470..22218480
-
Hg19::chr17:7154288..7154306,+p@chr17:7154288..7154306
+
Hg19::chr2:224701010..224701027,+p@chr2:224701010..224701027
+


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
leukocyte1.70e-39136
hematopoietic stem cell4.11e-33168
angioblastic mesenchymal cell4.11e-33168
hematopoietic cell1.30e-30177
hematopoietic oligopotent progenitor cell2.65e-26161
hematopoietic multipotent progenitor cell2.65e-26161
hematopoietic lineage restricted progenitor cell3.34e-21120
lymphoid lineage restricted progenitor cell2.03e-1952
lymphocyte6.39e-1953
common lymphoid progenitor6.39e-1953
nucleate cell5.57e-1855
nongranular leukocyte5.38e-17115
granulocyte1.18e-148
lymphocyte of B lineage4.85e-1424
pro-B cell4.85e-1424
dendritic cell9.15e-1310
histamine secreting cell1.79e-125
biogenic amine secreting cell1.79e-125
granulocytopoietic cell1.79e-125
mast cell1.79e-125
mast cell progenitor1.79e-125
basophil mast progenitor cell1.79e-125
mesenchymal cell3.03e-12354
connective tissue cell1.09e-11361
Langerhans cell2.98e-115
blood cell2.70e-1011
myeloid cell7.08e-10108
common myeloid progenitor7.08e-10108
motile cell9.46e-10386
myeloid leukocyte1.01e-0972
conventional dendritic cell9.14e-098
plasmacytoid dendritic cell1.19e-083
intermediate monocyte1.59e-089
CD14-positive, CD16-positive monocyte1.59e-089
stem cell2.74e-08441
basophil3.18e-083
neutrophil3.58e-083
single nucleate cell8.47e-083
mononuclear cell8.47e-083
natural killer cell1.09e-073
pro-NK cell1.09e-073
multi fate stem cell1.97e-07427
somatic stem cell4.07e-07433
Uber Anatomy
Ontology termp-valuen
connective tissue1.51e-11371
hematopoietic system4.49e-0798
blood island4.49e-0798


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)
MA0003.10.321379
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
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
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.12.20326
MA0055.10.465994
MA0056.10
MA0057.10.147053
MA0058.11.16137
MA0059.11.15845
MA0060.10.267412
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.216116
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
MA0093.11.02138
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.993014
MA0105.10.830067
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.11.12205
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.10.718193
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.658749
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.255126
MA0137.21.06611
MA0104.20.735746
MA0047.20.695777
MA0112.21.12726
MA0065.20.718489
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.318517
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.11.18186
MA0164.10.738243
MA0080.22.70673
MA0018.20.709805
MA0099.20.629739
MA0079.20.0607789
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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
EBF1#187957.422055705474179.7002838805275e-050.00137985283056172
IRF4#3662518.26209390562011.14070523243612e-064.66095906769937e-05
MEF2A#4205412.4954872730960.0001113336277199790.00154601419298589
MEF2C#4208213.77045149754130.008235596942270060.0324670658709702
NFKB1#479065.488063424193843.65870229532191e-050.000707351368050953
PAX5#507955.557971275981520.0003977176196612860.00388670632355245
POLR2A#543062.147453176558070.01019570676818780.038020117083685
SPI1#668856.836936257102270.0001449641773974030.00188565372066352
SRF#672236.89858913108390.00644245168930370.0280012989295929
TCF12#693858.862054085155354.06365504449859e-050.000743524998585123
ZEB1#6935411.25895467836260.0001672700379805450.00204824897369564



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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