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{{Coexpression_clusters
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|full_id=C4741_Nucleus_Chondrocyte_thyroid_hippocampus_Fibroblast_medial_insula
|id=C4741
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4741_Nucleus_Chondrocyte_thyroid_hippocampus_Fibroblast_medial_insula



Phase1 CAGE Peaks

Hg19::chr8:19459708..19459747,-p2@CSGALNACT1
Hg19::chr8:19459753..19459765,-p9@CSGALNACT1
Hg19::chr8:19459967..19459992,-p6@CSGALNACT1


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism6.93e-37114
neural tube1.49e-2956
neural rod1.49e-2956
future spinal cord1.49e-2956
neural keel1.49e-2956
tube7.79e-28192
anatomical conduit2.63e-27240
regional part of nervous system3.53e-2753
regional part of brain3.53e-2753
regional part of forebrain3.43e-2641
forebrain3.43e-2641
anterior neural tube3.43e-2641
future forebrain3.43e-2641
anatomical cluster5.05e-25373
telencephalon1.82e-2434
brain grey matter6.75e-2434
gray matter6.75e-2434
cerebral hemisphere2.78e-2332
brain8.46e-2368
future brain8.46e-2368
regional part of telencephalon1.08e-2232
central nervous system1.12e-2281
regional part of cerebral cortex3.35e-2122
structure with developmental contribution from neural crest3.95e-20132
neural plate4.02e-2082
presumptive neural plate4.02e-2082
neocortex1.52e-1920
nervous system2.39e-1989
neurectoderm2.51e-1886
cerebral cortex1.13e-1725
pallium1.13e-1725
multi-tissue structure4.79e-16342
organ system subdivision2.99e-15223
pre-chordal neural plate7.05e-1561
epithelium1.01e-14306
cell layer1.26e-14309
ecto-epithelium8.12e-14104
ectoderm-derived structure3.92e-11171
ectoderm3.92e-11171
presumptive ectoderm3.92e-11171
anatomical system4.06e-10624
anatomical group5.12e-10625
splanchnic layer of lateral plate mesoderm1.40e-0983
multi-cellular organism2.07e-09656
basal ganglion1.64e-089
nuclear complex of neuraxis1.64e-089
aggregate regional part of brain1.64e-089
collection of basal ganglia1.64e-089
cerebral subcortex1.64e-089
vessel1.74e-0868
germ layer2.10e-08560
germ layer / neural crest2.10e-08560
embryonic tissue2.10e-08560
presumptive structure2.10e-08560
germ layer / neural crest derived structure2.10e-08560
epiblast (generic)2.10e-08560
epithelial tube open at both ends4.08e-0859
blood vessel4.08e-0859
blood vasculature4.08e-0859
vascular cord4.08e-0859
embryonic structure4.92e-08564
circulatory system1.10e-07112
neural nucleus1.13e-079
nucleus of brain1.13e-079
gyrus1.30e-076
vasculature1.49e-0778
vascular system1.49e-0778
epithelial tube1.68e-07117
developing anatomical structure2.19e-07581
embryo3.62e-07592
systemic artery4.42e-0733
systemic arterial system4.42e-0733
cardiovascular system6.44e-07109
organ part9.44e-07218


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
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
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
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
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.12.08673
MA0153.11.43021
MA0154.13.19371
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
CTCF#1066435.360256373075030.0064925092527670.0281462444003874
RAD21#5885310.35503389545630.0009004912073565420.00668988484884833
SUZ12#23512350.11578091106297.93834897779404e-060.000223650722657629



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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