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{{Coexpression_clusters
{
|full_id=C3375_testis_parietal_brain_occipital_temporal_cerebellum_duodenum

Latest revision as of 12:24, 17 September 2013


Full id: C3375_testis_parietal_brain_occipital_temporal_cerebellum_duodenum



Phase1 CAGE Peaks

Hg19::chr13:45915545..45915601,+p1@ENST00000412946
p1@ENST00000520590
p1@ENST00000520622
Hg19::chr15:77197781..77197801,-p3@SCAPER
Hg19::chr22:42486923..42487002,+p1@LOC100132273


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
lymphoid lineage restricted progenitor cell1.36e-0752
lymphocyte2.37e-0753
common lymphoid progenitor2.37e-0753
nucleate cell6.72e-0755
Uber Anatomy
Ontology termp-valuen
adult organism1.13e-40114
neural tube7.41e-3156
neural rod7.41e-3156
future spinal cord7.41e-3156
neural keel7.41e-3156
regional part of nervous system3.98e-2953
regional part of brain3.98e-2953
nervous system2.46e-2789
central nervous system3.96e-2781
neurectoderm7.22e-2486
brain1.84e-2368
future brain1.84e-2368
regional part of forebrain2.79e-2341
forebrain2.79e-2341
anterior neural tube2.79e-2341
future forebrain2.79e-2341
neural plate1.02e-2282
presumptive neural plate1.02e-2282
telencephalon1.50e-1934
brain grey matter1.78e-1934
gray matter1.78e-1934
cerebral hemisphere9.57e-1932
regional part of telencephalon1.78e-1832
pre-chordal neural plate3.66e-1661
regional part of cerebral cortex7.34e-1622
ecto-epithelium1.29e-15104
cerebral cortex8.63e-1525
pallium8.63e-1525
neocortex1.03e-1420
ectoderm-derived structure6.17e-14171
ectoderm6.17e-14171
presumptive ectoderm6.17e-14171
structure with developmental contribution from neural crest5.28e-10132
posterior neural tube1.12e-0815
chordal neural plate1.12e-0815
organ system subdivision5.55e-08223
segmental subdivision of nervous system1.82e-0713
segmental subdivision of hindbrain4.51e-0712
hindbrain4.51e-0712
presumptive hindbrain4.51e-0712


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.886807
MA0058.11.70328
MA0059.11.70014
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.79391
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
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
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
MA0139.11.12079
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
MA0039.22.15877
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
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.90288
MA0102.21.88331
MA0258.11.29138
MA0259.11.40979
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
ATF3#467322.46317452600878.81932387510763e-050.00129401709214999
CCNT2#90536.336201576962630.003930750035764890.0189530749300669
CTCF#1066435.360256373075030.0064925092527670.0278754850503488
E2F1#186934.907389214879320.008460985347239390.0324194463323306
E2F6#187635.017155731697390.00791769806886330.0321132609170491
ELF1#199734.258097958807540.01295179875054610.0460829526695153
HNF4A#3172215.42152690863580.005444210486686610.0246718692623042
HNF4G#3174219.16894835096450.003543986611284220.0179692405911211
IRF1#365937.63716375356390.002244692747297240.0127777547192989
MAX#414936.452555509007120.003721913834265510.0186093909870191
MYC#460935.22228187160940.007020843755740150.029369939157484
SP1#666735.69838137814090.005403962701712170.0245833461366024
TRIM28#10155212.39368336350830.008368344129438470.0328972594773375



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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