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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:50, 17 September 2013


Full id: C1721_Mast_CD14_Eosinophils_Natural_Peripheral_Basophils_Neutrophils



Phase1 CAGE Peaks

Hg19::chr14:35874092..35874103,-p16@NFKBIA
Hg19::chr14:35874125..35874149,-p11@NFKBIA
Hg19::chr14:93121971..93122003,+p@chr14:93121971..93122003
+
Hg19::chr1:228297188..228297205,+p@chr1:228297188..228297205
+
Hg19::chr7:129592344..129592375,+p@chr7:129592344..129592375
+


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 monocyte2.95e-3942
CD14-positive, CD16-negative classical monocyte2.95e-3942
myeloid leukocyte7.19e-3572
leukocyte3.85e-34136
defensive cell1.90e-3248
phagocyte1.90e-3248
granulocyte monocyte progenitor cell2.24e-2967
hematopoietic lineage restricted progenitor cell9.95e-28120
myeloid lineage restricted progenitor cell6.76e-2766
macrophage dendritic cell progenitor8.40e-2561
nongranular leukocyte9.66e-25115
hematopoietic stem cell1.45e-23168
angioblastic mesenchymal cell1.45e-23168
monopoietic cell4.84e-2359
monocyte4.84e-2359
monoblast4.84e-2359
promonocyte4.84e-2359
hematopoietic oligopotent progenitor cell1.74e-22161
hematopoietic multipotent progenitor cell1.74e-22161
hematopoietic cell5.43e-22177
myeloid cell3.59e-20108
common myeloid progenitor3.59e-20108
stuff accumulating cell2.75e-1587
granulocyte2.52e-088
histamine secreting cell9.62e-085
biogenic amine secreting cell9.62e-085
granulocytopoietic cell9.62e-085
mast cell9.62e-085
mast cell progenitor9.62e-085
basophil mast progenitor cell9.62e-085
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.47e-2598
blood island1.47e-2598
immune system9.72e-2593
hemolymphoid system1.58e-24108
bone marrow5.70e-2476
bone element4.89e-2282
skeletal element1.22e-1990
skeletal system5.54e-17100


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)
MA0003.10.280184
MA0004.10.626788
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
MA0028.10.470679
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.860776
MA0061.13.99021
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
MA0074.10.730989
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
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.12.02769
MA0103.10.442769
MA0105.13.01153
MA0106.10.779931
MA0107.13.60303
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
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
MA0145.10.442008
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.11.57192
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.12.67024
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.21.83842
MA0099.20.699641
MA0079.20.823998
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
BCL11A#53335211.34778204144280.01157056933741320.0422864083364278
BCL3#602213.81884112149530.007902823332280840.032439687379636
CHD2#110636.206413700470110.007774550126275590.0319495648319075
CTBP2#1488225.08680013573130.002461438599678380.0138477798918235
CTCF#1066444.288205098460020.005152015588243280.0239302359804554
EBF1#187935.34388010794140.01187615563868110.0432307629133952
ELF1#199743.406478367046030.01235066105299550.0447319562253362
GATA3#2625210.89460654288240.0125158291218830.045279918167533
HNF4G#3174211.50136901057870.01127438304921050.0413733412254565
IRF4#3662313.14870761204650.0008860469322808430.00660277242671987
MEF2C#4208216.52454179704960.005579850077982050.0252427428872203
NFKB1#479044.390450739355070.004707732692524960.0222013408595057
RAD21#588536.21302033727380.007751055068811640.031890657119903
SMC3#912639.02695970695970.002650964449467550.0146357285054682
SRF#672238.278306957300690.003404846073776150.0173572860398842
TCF7L2#693436.462105937882410.006930108755689190.0293168190349734



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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