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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 12:24, 17 September 2013


Full id: C3337_kidney_umbilical_retina_putamen_Ciliary_brain_caudate



Phase1 CAGE Peaks

Hg19::chr12:80794469..80794483,+p@chr12:80794469..80794483
+
Hg19::chr12:80794499..80794508,+p@chr12:80794499..80794508
+
Hg19::chr3:64547432..64547444,-p@chr3:64547432..64547444
-


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
ciliated cell2.46e-233
ciliated epithelial cell2.46e-233
multi-ciliated epithelial cell2.46e-233
non-pigmented ciliary epithelial cell2.46e-233
Uber Anatomy
Ontology termp-valuen
gyrus3.29e-306
pre-chordal neural plate2.06e-2761
neural plate2.80e-2582
presumptive neural plate2.80e-2582
regional part of cerebral cortex2.19e-2422
neurectoderm5.79e-2486
ciliary epithelium2.46e-233
ciliary body2.46e-233
ecto-epithelium8.94e-22104
cerebral cortex2.02e-2125
pallium2.02e-2125
neocortex3.14e-2120
cerebral hemisphere1.86e-2032
regional part of nervous system2.21e-2053
regional part of brain2.21e-2053
telencephalon3.37e-1934
neural tube3.47e-1956
neural rod3.47e-1956
future spinal cord3.47e-1956
neural keel3.47e-1956
regional part of forebrain3.60e-1941
forebrain3.60e-1941
anterior neural tube3.60e-1941
future forebrain3.60e-1941
atypical epithelium1.17e-174
regional part of telencephalon1.35e-1632
middle temporal gyrus5.83e-162
brain grey matter1.43e-1534
gray matter1.43e-1534
brain3.45e-1568
future brain3.45e-1568
structure with developmental contribution from neural crest1.62e-14132
adult organism1.96e-13114
eye1.87e-1221
visual system1.87e-1221
central nervous system1.92e-1281
vasculature of eye5.88e-126
uvea5.88e-126
vasculature of head5.88e-126
ectoderm-derived structure9.75e-12171
ectoderm9.75e-12171
presumptive ectoderm9.75e-12171
pigment epithelium of eye4.06e-1111
nervous system5.36e-1189
sense organ7.81e-1124
sensory system7.81e-1124
entire sense organ system7.81e-1124
frontal cortex8.06e-113
temporal lobe3.60e-106
camera-type eye2.81e-0920
simple eye2.81e-0920
immature eye2.81e-0920
ocular region2.81e-0920
eyeball of camera-type eye2.81e-0920
optic cup2.81e-0920
optic vesicle2.81e-0920
eye primordium2.81e-0920
surface4.52e-091
anterior segment of eyeball9.16e-0914
occipital pole9.74e-091
pole of cerebral hemisphere9.74e-091
organ part1.33e-08218
paracentral gyrus1.78e-081
postcentral gyrus1.91e-081
face2.05e-0822
multi-tissue structure2.76e-07342
limbic system8.17e-075
epithelium9.66e-07306
vasculature of organ9.90e-0711


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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
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
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.31555
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
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
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
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
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
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
MA0079.20.181755
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


No analysis results for this cluster

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.