Personal tools

Coexpression cluster:C3319

From FANTOM5_SSTAR

Jump to: navigation, search


Full id: C3319_duodenum_lens_acute_putamen_Neural_temporal_brain



Phase1 CAGE Peaks

Hg19::chr12:6809890..6809929,-p3@C12orf53
Hg19::chr19:42574335..42574367,-p@chr19:42574335..42574367
-
Hg19::chr19:42574371..42574384,-p@chr19:42574371..42574384
-


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>disease_data<br>


Cell Type
Ontology termp-valuen
neural cell4.58e-0725
Uber Anatomy
Ontology termp-valuen
neurectoderm1.70e-4986
neural plate8.77e-4782
presumptive neural plate8.77e-4782
nervous system2.94e-4589
central nervous system8.02e-4481
adult organism1.48e-43114
neural tube6.67e-4256
neural rod6.67e-4256
future spinal cord6.67e-4256
neural keel6.67e-4256
regional part of nervous system6.61e-4053
regional part of brain6.61e-4053
pre-chordal neural plate3.67e-3661
brain3.26e-3568
future brain3.26e-3568
ecto-epithelium4.25e-33104
regional part of forebrain1.56e-3241
forebrain1.56e-3241
anterior neural tube1.56e-3241
future forebrain1.56e-3241
ectoderm-derived structure2.19e-32171
ectoderm2.19e-32171
presumptive ectoderm2.19e-32171
structure with developmental contribution from neural crest9.56e-30132
telencephalon1.52e-2734
brain grey matter2.42e-2734
gray matter2.42e-2734
cerebral hemisphere1.06e-2632
regional part of telencephalon4.46e-2632
anatomical cluster7.97e-24373
cerebral cortex6.92e-2125
pallium6.92e-2125
organ system subdivision1.68e-19223
regional part of cerebral cortex1.01e-1822
tube1.63e-17192
neocortex4.90e-1720
cell layer2.79e-14309
epithelium3.44e-14306
organ part1.61e-13218
multi-tissue structure2.74e-13342
anatomical conduit4.55e-13240
embryo9.09e-11592
posterior neural tube2.34e-1015
chordal neural plate2.34e-1015
developing anatomical structure4.29e-09581
segmental subdivision of nervous system6.25e-0913
segmental subdivision of hindbrain1.61e-0812
hindbrain1.61e-0812
presumptive hindbrain1.61e-0812
basal ganglion2.18e-089
nuclear complex of neuraxis2.18e-089
aggregate regional part of brain2.18e-089
collection of basal ganglia2.18e-089
cerebral subcortex2.18e-089
neural nucleus7.08e-089
nucleus of brain7.08e-089
multi-cellular organism1.82e-07656
germ layer4.71e-07560
germ layer / neural crest4.71e-07560
embryonic tissue4.71e-07560
presumptive structure4.71e-07560
germ layer / neural crest derived structure4.71e-07560
epiblast (generic)4.71e-07560
embryonic structure5.13e-07564
eye6.59e-0721
visual system6.59e-0721
regional part of metencephalon7.84e-079
metencephalon7.84e-079
future metencephalon7.84e-079
sense organ9.44e-0724
sensory system9.44e-0724
entire sense organ system9.44e-0724
Disease
Ontology termp-valuen
germ cell and embryonal cancer6.30e-0822
germ cell cancer6.30e-0822


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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
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
MA0057.12.4146
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.12.75836
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
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.12.3269
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
MA0139.10.440097
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
MA0149.111.4925
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
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
MA0162.10.455568
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.29.48295
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


No analysis results for this cluster

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.