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{{Coexpression_clusters
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|full_id=C4673_retina_substantia_optic_Astrocyte_melanoma_Neural_thalamus
|id=C4673
}}

Latest revision as of 14:17, 17 September 2013


Full id: C4673_retina_substantia_optic_Astrocyte_melanoma_Neural_thalamus



Phase1 CAGE Peaks

Hg19::chr7:20371077..20371122,+p6@ITGB8
Hg19::chr7:20371123..20371138,+p17@ITGB8
Hg19::chr7:20371139..20371164,+p4@ITGB8


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
neural cell1.18e-0825
neurectodermal cell1.61e-0759
neuronal stem cell1.96e-078
Uber Anatomy
Ontology termp-valuen
central nervous system4.21e-5081
nervous system1.66e-4989
neural tube1.26e-4356
neural rod1.26e-4356
future spinal cord1.26e-4356
neural keel1.26e-4356
regional part of nervous system1.13e-4053
regional part of brain1.13e-4053
brain2.01e-3968
future brain2.01e-3968
adult organism6.39e-36114
neural plate1.74e-3482
presumptive neural plate1.74e-3482
regional part of forebrain2.78e-3341
forebrain2.78e-3341
anterior neural tube2.78e-3341
future forebrain2.78e-3341
ectoderm-derived structure2.26e-32171
ectoderm2.26e-32171
presumptive ectoderm2.26e-32171
neurectoderm1.25e-3186
brain grey matter1.07e-2934
gray matter1.07e-2934
telencephalon1.14e-2934
regional part of telencephalon8.52e-2832
cerebral hemisphere1.16e-2732
ecto-epithelium1.86e-26104
pre-chordal neural plate1.48e-2561
organ system subdivision3.68e-24223
structure with developmental contribution from neural crest1.18e-21132
cerebral cortex1.55e-2125
pallium1.55e-2125
regional part of cerebral cortex1.44e-1822
anatomical cluster4.50e-18373
neocortex6.13e-1720
embryo3.55e-13592
anatomical conduit5.69e-13240
developing anatomical structure1.25e-11581
multi-cellular organism1.28e-11656
anatomical system1.94e-11624
organ2.34e-11503
anatomical group2.55e-11625
posterior neural tube3.05e-1115
chordal neural plate3.05e-1115
embryonic structure5.32e-10564
germ layer9.87e-10560
germ layer / neural crest9.87e-10560
embryonic tissue9.87e-10560
presumptive structure9.87e-10560
germ layer / neural crest derived structure9.87e-10560
epiblast (generic)9.87e-10560
neural nucleus1.37e-099
nucleus of brain1.37e-099
segmental subdivision of nervous system1.74e-0913
basal ganglion2.35e-099
nuclear complex of neuraxis2.35e-099
aggregate regional part of brain2.35e-099
collection of basal ganglia2.35e-099
cerebral subcortex2.35e-099
tube5.17e-09192
segmental subdivision of hindbrain1.52e-0812
hindbrain1.52e-0812
presumptive hindbrain1.52e-0812
telencephalic nucleus9.72e-087
organ part1.04e-07218
multi-tissue structure1.70e-07342
brainstem3.76e-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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.886807
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
MA0070.12.89432
MA0071.10.897953
MA0072.11.29561
MA0073.10.0834661
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
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
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
MA0145.12.94723
MA0146.10.707589
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
MA0152.10.902317
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.032764436361896
SMARCB1#6598318.25271578115740.000164397760679890.00204010666915958



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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