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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0.

Latest revision as of 11:48, 17 September 2013


Full id: C1596_heart_optic_left_corpus_substantia_spinal_medulla



Phase1 CAGE Peaks

Hg19::chr10:88426533..88426556,+p2@LDB3
Hg19::chr11:111781454..111781513,-p4@CRYAB
Hg19::chr20:44036838..44036847,+p22@DBNDD2
Hg19::chrX:10124977..10125036,+p2@CLCN4
Hg19::chrX:10125040..10125059,+p3@CLCN4


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


GO IDGO nameFDR corrected p-value
GO:0032387negative regulation of intracellular transport0.0240187203952639



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 organism1.91e-86114
neural tube2.19e-4756
neural rod2.19e-4756
future spinal cord2.19e-4756
neural keel2.19e-4756
regional part of nervous system1.44e-4353
regional part of brain1.44e-4353
neural plate6.24e-4182
presumptive neural plate6.24e-4182
central nervous system2.69e-4081
brain2.03e-3968
future brain2.03e-3968
nervous system1.13e-3889
neurectoderm4.28e-3886
regional part of forebrain1.56e-3541
forebrain1.56e-3541
anterior neural tube1.56e-3541
future forebrain1.56e-3541
structure with developmental contribution from neural crest2.00e-33132
ecto-epithelium1.59e-30104
brain grey matter1.06e-2734
gray matter1.06e-2734
telencephalon1.25e-2734
pre-chordal neural plate3.97e-2761
regional part of telencephalon3.71e-2532
cerebral hemisphere5.57e-2532
ectoderm-derived structure7.95e-24171
ectoderm7.95e-24171
presumptive ectoderm7.95e-24171
organ system subdivision6.41e-19223
regional part of cerebral cortex1.70e-1822
cerebral cortex4.01e-1725
pallium4.01e-1725
neocortex3.04e-1620
tube1.77e-15192
multi-tissue structure4.32e-15342
cell layer5.78e-15309
epithelium7.47e-15306
anatomical cluster1.41e-14373
anatomical conduit2.76e-13240
neural nucleus9.40e-139
nucleus of brain9.40e-139
posterior neural tube1.22e-1215
chordal neural plate1.22e-1215
basal ganglion2.56e-129
nuclear complex of neuraxis2.56e-129
aggregate regional part of brain2.56e-129
collection of basal ganglia2.56e-129
cerebral subcortex2.56e-129
segmental subdivision of nervous system2.06e-1013
organ part3.38e-10218
telencephalic nucleus4.17e-107
brainstem1.53e-096
diencephalon1.80e-097
future diencephalon1.80e-097
segmental subdivision of hindbrain3.88e-0912
hindbrain3.88e-0912
presumptive hindbrain3.88e-0912
gyrus9.19e-096
embryo1.45e-08592
organ1.63e-08503
germ layer2.36e-08560
germ layer / neural crest2.36e-08560
embryonic tissue2.36e-08560
presumptive structure2.36e-08560
germ layer / neural crest derived structure2.36e-08560
epiblast (generic)2.36e-08560
embryonic structure4.61e-08564
developing anatomical structure5.10e-08581
multi-cellular organism8.70e-08656
limbic system2.26e-075


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)
MA0003.10.481059
MA0004.11.51734
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.189508
MA0058.12.23895
MA0059.11.29682
MA0060.10.860776
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.143081
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.21.35805
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.11.66846
MA0153.11.21379
MA0154.10.98952
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0442129
MA0102.21.66336
MA0258.10.914277
MA0259.10.395396
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
SETDB1#9869216.12801047120420.00585057846659340.0262661120436981



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.