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{{Coexpression_clusters
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|full_id=C3684_salivary_parotid_seminal_submaxillary_Dendritic_medulla_Alveolar
|id=C3684
}}

Latest revision as of 12:31, 17 September 2013


Full id: C3684_salivary_parotid_seminal_submaxillary_Dendritic_medulla_Alveolar



Phase1 CAGE Peaks

Hg19::chr17:7462031..7462086,+p2@TNFSF13
Hg19::chr17:7462091..7462102,+p9@TNFSF13
Hg19::chr17:7462103..7462110,+p14@TNFSF13


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
macrophage dendritic cell progenitor9.55e-0861
monopoietic cell7.99e-0759
monocyte7.99e-0759
monoblast7.99e-0759
promonocyte7.99e-0759
granulocyte monocyte progenitor cell9.76e-0767
Uber Anatomy
Ontology termp-valuen
adult organism1.69e-51114
neural tube1.12e-2656
neural rod1.12e-2656
future spinal cord1.12e-2656
neural keel1.12e-2656
regional part of nervous system1.28e-2453
regional part of brain1.28e-2453
regional part of forebrain9.71e-2041
forebrain9.71e-2041
anterior neural tube9.71e-2041
future forebrain9.71e-2041
brain grey matter2.10e-1834
gray matter2.10e-1834
brain2.18e-1868
future brain2.18e-1868
telencephalon5.47e-1834
central nervous system1.67e-1781
cerebral hemisphere7.32e-1732
neural plate1.07e-1682
presumptive neural plate1.07e-1682
regional part of telencephalon1.14e-1632
neurectoderm6.45e-1686
organ system subdivision2.98e-14223
nervous system4.11e-1489
regional part of cerebral cortex5.22e-1422
organ1.83e-13503
neocortex1.33e-1220
pre-chordal neural plate4.83e-1261
ecto-epithelium1.37e-11104
cerebral cortex1.46e-1125
pallium1.46e-1125
tube2.23e-11192
anatomical conduit1.46e-10240
developing anatomical structure6.72e-10581
anatomical cluster7.74e-10373
embryo1.16e-09592
structure with developmental contribution from neural crest2.90e-09132
neural nucleus7.80e-099
nucleus of brain7.80e-099
basal ganglion1.02e-089
nuclear complex of neuraxis1.02e-089
aggregate regional part of brain1.02e-089
collection of basal ganglia1.02e-089
cerebral subcortex1.02e-089
embryonic structure1.04e-08564
anatomical system2.20e-08624
germ layer2.44e-08560
germ layer / neural crest2.44e-08560
embryonic tissue2.44e-08560
presumptive structure2.44e-08560
germ layer / neural crest derived structure2.44e-08560
epiblast (generic)2.44e-08560
anatomical group2.72e-08625
posterior neural tube4.20e-0815
chordal neural plate4.20e-0815
multi-cellular organism7.96e-08656
multi-tissue structure2.01e-07342
telencephalic nucleus5.46e-077
brainstem5.73e-076


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.12.94911
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.13.3282
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.14.65896
MA0117.11.36676
MA0119.11.66081
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.13.48527
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CEBPB#105137.971147625824820.001974187055288560.0115172674487365
STAT1#6772320.70658749719920.0001125992441046670.00154794688101189
STAT3#6774310.51946499715420.0008589184530415310.00642444920985494
TFAP2C#7022310.80922860986020.0007916746575753130.00615282851335825



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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