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{{Coexpression_clusters
{
|full_id=C3255_pituitary_smallcell_maxillary_neuroblastoma_argyrophil_gastrointestinal_small
 

Latest revision as of 12:22, 17 September 2013


Full id: C3255_pituitary_smallcell_maxillary_neuroblastoma_argyrophil_gastrointestinal_small



Phase1 CAGE Peaks

Hg19::chr12:131118370..131118390,-p5@ENST00000541840
Hg19::chr12:131118436..131118449,-p2@ENST00000541840
Hg19::chr12:131118454..131118470,-p1@ENST00000541840


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
nervous system5.60e-5889
neural tube2.66e-5656
neural rod2.66e-5656
future spinal cord2.66e-5656
neural keel2.66e-5656
central nervous system4.24e-5581
regional part of nervous system9.94e-5453
regional part of brain9.94e-5453
regional part of forebrain2.21e-4741
forebrain2.21e-4741
anterior neural tube2.21e-4741
future forebrain2.21e-4741
brain6.66e-4668
future brain6.66e-4668
brain grey matter7.11e-4134
gray matter7.11e-4134
telencephalon1.32e-4034
neural plate9.02e-3982
presumptive neural plate9.02e-3982
cerebral hemisphere2.19e-3732
regional part of telencephalon5.22e-3732
neurectoderm2.16e-3686
regional part of cerebral cortex2.57e-3322
pre-chordal neural plate4.12e-3361
adult organism5.63e-32114
cerebral cortex1.09e-3125
pallium1.09e-3125
ecto-epithelium1.58e-31104
neocortex1.59e-2920
organ system subdivision1.59e-28223
ectoderm-derived structure3.82e-27171
ectoderm3.82e-27171
presumptive ectoderm3.82e-27171
structure with developmental contribution from neural crest7.70e-22132
anatomical cluster1.96e-13373
brainstem2.88e-136
gyrus6.54e-136
tube7.45e-13192
limbic system2.63e-115
temporal lobe5.48e-116
neural nucleus1.58e-109
nucleus of brain1.58e-109
basal ganglion1.79e-109
nuclear complex of neuraxis1.79e-109
aggregate regional part of brain1.79e-109
collection of basal ganglia1.79e-109
cerebral subcortex1.79e-109
organ part1.92e-10218
posterior neural tube2.09e-1015
chordal neural plate2.09e-1015
gland of diencephalon4.26e-104
neuroendocrine gland4.26e-104
segmental subdivision of nervous system1.01e-0913
segmental subdivision of hindbrain4.29e-0812
hindbrain4.29e-0812
presumptive hindbrain4.29e-0812
diencephalon4.46e-087
future diencephalon4.46e-087
anatomical conduit5.62e-08240
multi-tissue structure9.34e-08342
medulla oblongata1.57e-073
myelencephalon1.57e-073
future myelencephalon1.57e-073
pons2.14e-073
frontal cortex2.23e-073
parietal lobe2.50e-075
epithelium3.82e-07306
embryo4.75e-07592
cell layer5.88e-07309
occipital lobe6.12e-075
telencephalic nucleus6.14e-077


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
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
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
MA0055.10.190716
MA0056.10
MA0057.10.333427
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
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
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
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.22.23118
MA0112.20.264678
MA0065.20.277623
MA0150.12.94916
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.22.08754
MA0079.20.09178
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
NANOG#79923329.24477848101273.99627955670032e-050.000734801832081382



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.