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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:41, 17 September 2013


Full id: C1272_medulloblastoma_neuroblastoma_colon_Osteoblast_normal_Ciliary_pons



Phase1 CAGE Peaks

Hg19::chr4:151502879..151502889,-p8@LRBA
Hg19::chr4:151502911..151502924,-p5@LRBA
Hg19::chr4:151502958..151502978,-p6@LRBA
Hg19::chr4:151503105..151503132,+p2@MAB21L2
Hg19::chr4:151503215..151503245,+p4@MAB21L2
Hg19::chr4:151503507..151503518,+p6@MAB21L2
Hg19::chr4:151513323..151513325,+p@chr4:151513323..151513325
+


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>

Uber Anatomy
Ontology termp-valuen
pigment epithelium of eye3.21e-2311
intestine1.01e-2017
eye8.06e-1721
visual system8.06e-1721
face2.99e-1622
subdivision of head6.12e-1649
camera-type eye9.53e-1520
simple eye9.53e-1520
immature eye9.53e-1520
ocular region9.53e-1520
eyeball of camera-type eye9.53e-1520
optic cup9.53e-1520
optic vesicle9.53e-1520
eye primordium9.53e-1520
sense organ2.03e-1424
sensory system2.03e-1424
entire sense organ system2.03e-1424
large intestine2.51e-1411
atypical epithelium8.25e-144
gastrointestinal system1.38e-1325
head2.05e-1356
colon4.75e-139
brainstem1.61e-126
anterior region of body1.03e-1162
craniocervical region1.03e-1162
ciliary epithelium3.61e-113
ciliary body3.61e-113
pigmented layer of retina1.09e-103
presumptive retinal pigmented epithelium1.09e-103
organ segment1.31e-1098
pons9.50e-103
vasculature of eye3.24e-096
uvea3.24e-096
vasculature of head3.24e-096
retina5.07e-096
photoreceptor array5.07e-096
posterior segment of eyeball5.07e-096
ectodermal placode8.53e-0931
layer of retina4.08e-084
anterior segment of eyeball4.35e-0814
ectoderm-derived structure4.90e-08171
ectoderm4.90e-08171
presumptive ectoderm4.90e-08171
neural plate2.96e-0782
presumptive neural plate2.96e-0782
sympathetic nervous system3.94e-075
autonomic nervous system3.94e-075
locus ceruleus5.85e-072
brainstem nucleus5.85e-072
hindbrain nucleus5.85e-072
posterior neural tube8.06e-0715
chordal neural plate8.06e-0715
small intestine8.93e-074
neurectoderm9.39e-0786
anatomical cluster9.40e-07373


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)
MA0003.10.00215847
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.912418
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.11.22641
MA0043.10.973609
MA0046.10.962263
MA0048.10.120314
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.13.85869
MA0058.10.406232
MA0059.11.04442
MA0060.11.86058
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.000265001
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.84202
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.12.96741
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.12.37413
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.11.30855
MA0145.10.0807715
MA0146.10.0127148
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.854285
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.071478
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.0167306
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.23.31082
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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
EP300#203354.838529804445140.001132708190785470.00775781433126394
YY1#752853.507979107038470.005072570672808980.0236168958852308



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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