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Coexpression cluster:C4244: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 12:42, 17 September 2013


Full id: C4244_parotid_pancreas_salivary_heart_submaxillary_left_umbilical



Phase1 CAGE Peaks

Hg19::chr2:71453519..71453532,-p@chr2:71453519..71453532
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Hg19::chr2:71453533..71453553,-p@chr2:71453533..71453553
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Hg19::chr2:71453567..71453584,-p@chr2:71453567..71453584
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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 organism9.32e-75114
neural tube2.96e-2656
neural rod2.96e-2656
future spinal cord2.96e-2656
neural keel2.96e-2656
regional part of nervous system3.96e-2453
regional part of brain3.96e-2453
neural plate1.10e-2382
presumptive neural plate1.10e-2382
neurectoderm4.39e-2286
central nervous system8.15e-2281
brain3.95e-2168
future brain3.95e-2168
nervous system4.54e-2089
structure with developmental contribution from neural crest1.11e-18132
regional part of forebrain3.43e-1841
forebrain3.43e-1841
anterior neural tube3.43e-1841
future forebrain3.43e-1841
ecto-epithelium1.24e-17104
organ system subdivision3.26e-15223
telencephalon1.06e-1434
brain grey matter1.67e-1434
gray matter1.67e-1434
ectoderm-derived structure4.21e-14171
ectoderm4.21e-14171
presumptive ectoderm4.21e-14171
pre-chordal neural plate6.11e-1461
anatomical cluster8.40e-14373
cerebral hemisphere2.43e-1232
anatomical conduit2.82e-12240
regional part of telencephalon3.44e-1232
multi-tissue structure3.53e-12342
regional part of cerebral cortex6.50e-1122
neocortex1.92e-1020
tube2.32e-10192
organ2.06e-09503
posterior neural tube2.57e-0915
chordal neural plate2.57e-0915
cerebral cortex2.66e-0925
pallium2.66e-0925
compound organ4.61e-0968
segmental subdivision of nervous system9.80e-0913
brainstem5.22e-086
valve1.92e-073
cardiac mesenchyme1.92e-073
cardial valve1.92e-073
tunica intima1.92e-073
heart layer1.92e-073
endocardium1.92e-073
endocardial cushion1.92e-073
presumptive endocardium1.92e-073
cardiac chamber2.63e-073
segmental subdivision of hindbrain3.04e-0712
hindbrain3.04e-0712
presumptive hindbrain3.04e-0712
organ part3.06e-07218
neural nucleus4.58e-079
nucleus of brain4.58e-079
epithelium5.98e-07306
embryo8.63e-07592
cell layer9.31e-07309


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
MA0014.11.24048
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
MA0048.10.904546
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
MA0068.14.85157
MA0069.12.91799
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
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
MA0103.11.52002
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.24.2163
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
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
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#1066435.360256373075030.0064925092527670.0280310530735731
E2F6#187635.017155731697390.00791769806886330.0323241524749439



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.