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Coexpression cluster:C2132

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Full id: C2132_cerebellum_putamen_pituitary_merkel_gastrointestinal_brain_iPS



Phase1 CAGE Peaks

  Short description
Hg19::chr11:45907236..45907257,+ p3@MAPK8IP1
Hg19::chr8:104511921..104511933,+ p@chr8:104511921..104511933
+
Hg19::chr8:104511965..104511977,+ p@chr8:104511965..104511977
+
Hg19::chr8:104512000..104512015,+ p@chr8:104512000..104512015
+


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
embryonic stem cell3.98e-075
Uber Anatomy
Ontology termp-valuen
neural tube2.95e-4756
neural rod2.95e-4756
future spinal cord2.95e-4756
neural keel2.95e-4756
nervous system4.77e-4789
regional part of nervous system1.12e-4653
regional part of brain1.12e-4653
central nervous system8.37e-4681
regional part of forebrain1.70e-4041
forebrain1.70e-4041
anterior neural tube1.70e-4041
future forebrain1.70e-4041
brain2.03e-4068
future brain2.03e-4068
brain grey matter9.40e-3334
gray matter9.40e-3334
telencephalon1.07e-3234
cerebral hemisphere2.99e-3132
neural plate8.57e-3182
presumptive neural plate8.57e-3182
regional part of telencephalon8.71e-3132
neurectoderm1.68e-2886
regional part of cerebral cortex3.23e-2722
pre-chordal neural plate4.05e-2761
neocortex3.08e-2520
ecto-epithelium3.85e-25104
organ system subdivision8.74e-25223
adult organism8.96e-24114
cerebral cortex4.59e-2325
pallium4.59e-2325
ectoderm-derived structure9.36e-23171
ectoderm9.36e-23171
presumptive ectoderm9.36e-23171
structure with developmental contribution from neural crest9.56e-17132
basal ganglion2.35e-119
nuclear complex of neuraxis2.35e-119
aggregate regional part of brain2.35e-119
collection of basal ganglia2.35e-119
cerebral subcortex2.35e-119
neural nucleus3.71e-119
nucleus of brain3.71e-119
anatomical cluster9.69e-10373
tube1.69e-09192
telencephalic nucleus2.87e-097
diencephalon3.73e-097
future diencephalon3.73e-097
temporal lobe4.12e-096
organ part1.12e-08218
posterior neural tube1.81e-0815
chordal neural plate1.81e-0815
gyrus2.72e-086
anatomical conduit9.44e-08240
segmental subdivision of hindbrain1.03e-0712
hindbrain1.03e-0712
presumptive hindbrain1.03e-0712
parietal lobe1.53e-075
occipital lobe2.89e-075
brainstem3.15e-076
segmental subdivision of nervous system6.07e-0713
limbic system6.11e-075
Disease
Ontology termp-valuen
respiratory system cancer2.09e-0716


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.13.49532
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.12.45009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.93422
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.11.90157
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.11.15856
MA0117.11.24497
MA0119.11.43218
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.27.89088
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.13.88191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.12.80246
MA0163.13.83423
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.211.2591
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066445.360256373075030.001211145381643620.00815753982416344
JUND#372735.245997956403270.01043432751748420.0386655808827183



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.