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Coexpression cluster:C4166: Difference between revisions

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{{Coexpression_clusters
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A0018.2;0.987913,MA0099.2;0.902716,MA0079.2;2.70224,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4166_neuroectodermal_Neural_small_Neurons_occipital_parietal_duodenum
|id=C4166
}}

Latest revision as of 12:40, 17 September 2013


Full id: C4166_neuroectodermal_Neural_small_Neurons_occipital_parietal_duodenum



Phase1 CAGE Peaks

Hg19::chr2:197791393..197791421,-p3@PGAP1
Hg19::chr2:197791423..197791438,-p2@PGAP1
Hg19::chr2:197791602..197791620,-p5@PGAP1


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 cell9.69e-0725
Uber Anatomy
Ontology termp-valuen
nervous system3.01e-3089
central nervous system8.12e-3081
ectoderm-derived structure2.81e-25171
ectoderm2.81e-25171
presumptive ectoderm2.81e-25171
brain1.83e-2468
future brain1.83e-2468
neural tube3.68e-2356
neural rod3.68e-2356
future spinal cord3.68e-2356
neural keel3.68e-2356
regional part of nervous system2.83e-2253
regional part of brain2.83e-2253
neurectoderm2.95e-1986
regional part of forebrain3.98e-1941
forebrain3.98e-1941
anterior neural tube3.98e-1941
future forebrain3.98e-1941
organ system subdivision1.71e-18223
neural plate1.28e-1782
presumptive neural plate1.28e-1782
ecto-epithelium2.95e-17104
brain grey matter5.07e-1634
gray matter5.07e-1634
telencephalon5.72e-1634
cerebral hemisphere2.90e-1532
regional part of telencephalon5.00e-1532
pre-chordal neural plate9.51e-1461
anatomical cluster1.78e-13373
structure with developmental contribution from neural crest4.67e-13132
cerebral cortex7.33e-1325
pallium7.33e-1325
regional part of cerebral cortex3.42e-1122
neocortex4.53e-1020
multi-cellular organism1.10e-09656
anatomical group9.04e-09625
anatomical system1.21e-08624
embryo2.41e-08592
embryonic structure3.19e-08564
anatomical conduit3.93e-08240
germ layer5.92e-08560
germ layer / neural crest5.92e-08560
embryonic tissue5.92e-08560
presumptive structure5.92e-08560
germ layer / neural crest derived structure5.92e-08560
epiblast (generic)5.92e-08560
adult organism8.06e-08114
tube1.79e-07192
epithelium4.15e-07306
developing anatomical structure4.83e-07581
cell layer6.12e-07309
organ6.30e-07503


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.12.26702
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
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
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
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
MA0145.10.752137
MA0146.11.16674
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
MA0104.21.2307
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
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.70224
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
CHD2#1106310.34402283411690.0009033701102746880.0066148125181924
E2F1#186934.907389214879320.008460985347239390.0326217088260608
ELF1#199734.258097958807540.01295179875054610.0463418722706596
HDAC2#3066313.41562023662630.0004140761399857210.00392108967122756
HNF4A#3172215.42152690863580.005444210486686610.0246815079662744
NANOG#79923219.49651898734180.003427255648501020.0174536352971425
NRF1#4899312.21027944771090.0005492172401020010.00472018592322358
PAX5#507936.669565531177830.003370290999677260.0173248915546239
SP1#666735.69838137814090.005403962701712170.0247049446532772
TRIM28#10155318.59052504526250.0001555969297255280.00197429082050837
YY1#752834.911170749853860.008441455341808260.0330107145858057
ZNF263#1012738.221841637010680.001799043925565870.0109652960923358



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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