Personal tools

Coexpression cluster:C2328

From FANTOM5_SSTAR

Revision as of 12:03, 17 September 2013 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Full id: C2328_anaplastic_hairy_Wilms_occipital_insula_pituitary_brain



Phase1 CAGE Peaks

Hg19::chr15:27216258..27216294,+p4@GABRG3
Hg19::chr15:27216297..27216341,+p1@GABRG3
Hg19::chr15:27216530..27216551,+p2@GABRG3
Hg19::chr15:27216555..27216580,+p3@GABRG3


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
neural tube1.39e-6556
neural rod1.39e-6556
future spinal cord1.39e-6556
neural keel1.39e-6556
regional part of nervous system2.09e-6153
regional part of brain2.09e-6153
central nervous system5.23e-5681
nervous system2.11e-5489
neural plate4.35e-5382
presumptive neural plate4.35e-5382
brain4.47e-5368
future brain4.47e-5368
regional part of forebrain6.79e-5141
forebrain6.79e-5141
anterior neural tube6.79e-5141
future forebrain6.79e-5141
neurectoderm8.86e-5086
cerebral hemisphere2.93e-4732
telencephalon7.28e-4734
brain grey matter7.88e-4734
gray matter7.88e-4734
pre-chordal neural plate7.12e-4461
regional part of telencephalon8.61e-4432
ecto-epithelium1.49e-41104
structure with developmental contribution from neural crest1.15e-37132
cerebral cortex2.60e-3625
pallium2.60e-3625
adult organism1.12e-34114
ectoderm-derived structure2.11e-33171
ectoderm2.11e-33171
presumptive ectoderm2.11e-33171
regional part of cerebral cortex3.11e-3222
neocortex3.29e-2920
organ system subdivision8.47e-26223
anatomical cluster2.63e-16373
posterior neural tube2.83e-1515
chordal neural plate2.83e-1515
organ part3.42e-15218
tube8.16e-14192
multi-tissue structure8.25e-14342
neural nucleus8.16e-129
nucleus of brain8.16e-129
embryo1.50e-11592
gyrus1.53e-116
segmental subdivision of hindbrain1.64e-1112
hindbrain1.64e-1112
presumptive hindbrain1.64e-1112
cell layer2.21e-11309
epithelium3.49e-11306
segmental subdivision of nervous system1.90e-1013
anatomical conduit3.08e-10240
occipital lobe4.05e-105
parietal lobe5.48e-105
brainstem9.69e-106
organ1.21e-09503
developing anatomical structure1.21e-09581
basal ganglion5.04e-099
nuclear complex of neuraxis5.04e-099
aggregate regional part of brain5.04e-099
collection of basal ganglia5.04e-099
cerebral subcortex5.04e-099
telencephalic nucleus6.24e-097
embryonic structure2.73e-08564
germ layer4.87e-08560
germ layer / neural crest4.87e-08560
embryonic tissue4.87e-08560
presumptive structure4.87e-08560
germ layer / neural crest derived structure4.87e-08560
epiblast (generic)4.87e-08560
corpus striatum6.82e-084
striatum6.82e-084
ventral part of telencephalon6.82e-084
future corpus striatum6.82e-084
regional part of metencephalon7.37e-089
metencephalon7.37e-089
future metencephalon7.37e-089
multi-cellular organism1.50e-07656
anatomical system4.57e-07624
anatomical group5.18e-07625


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)
MA0003.12.39007
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.13.20189
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.599068
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.14.42006
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.11.70272
MA0146.12.92476
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.24.85059
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.13.05999
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.13.50007
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.72671
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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.