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Coexpression cluster:C2830

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Full id: C2830_mature_Hepatocyte_mesenchymal_liver_pleomorphic_pancreas_chorionic



Phase1 CAGE Peaks

  Short description
Hg19::chr5:78365455..78365489,+ p3@BHMT2
Hg19::chr5:78365536..78365543,+ p4@BHMT2
Hg19::chr5:78365545..78365572,+ p2@BHMT2
Hg19::chr7:150038704..150038758,- p1@RARRES2


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


GO IDGO nameFDR corrected p-value
GO:0047150betaine-homocysteine S-methyltransferase activity0.00185441379597977
GO:0008898homocysteine S-methyltransferase activity0.00185441379597977
GO:0008172S-methyltransferase activity0.00271948664090565
GO:0001523retinoid metabolic process0.00271948664090565
GO:0016101diterpenoid metabolic process0.00271948664090565
GO:0006721terpenoid metabolic process0.0028841766369992
GO:0006720isoprenoid metabolic process0.00794257461958667
GO:0019748secondary metabolic process0.00818429998071893
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0117988707879793
GO:0008168methyltransferase activity0.0311175964910053
GO:0016741transferase activity, transferring one-carbon groups0.0311175964910053



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


Cell Type
Ontology termp-valuen
fat cell4.73e-1115
fibroblast1.82e-0776
Uber Anatomy
Ontology termp-valuen
adult organism6.77e-36114
structure with developmental contribution from neural crest6.42e-19132
neural plate1.57e-1882
presumptive neural plate1.57e-1882
multi-tissue structure1.95e-18342
neurectoderm1.78e-1686
neural tube2.06e-1656
neural rod2.06e-1656
future spinal cord2.06e-1656
neural keel2.06e-1656
regional part of nervous system2.54e-1553
regional part of brain2.54e-1553
pre-chordal neural plate4.79e-1561
anatomical cluster9.38e-14373
regional part of forebrain3.43e-1341
forebrain3.43e-1341
anterior neural tube3.43e-1341
future forebrain3.43e-1341
cell layer4.94e-13309
epithelium1.15e-12306
brain1.45e-1268
future brain1.45e-1268
ecto-epithelium2.52e-12104
central nervous system3.34e-1281
multi-cellular organism4.41e-12656
nervous system4.96e-1289
tissue8.85e-12773
organ system subdivision1.15e-11223
anatomical system1.59e-10624
anatomical group2.24e-10625
brain grey matter3.49e-1034
gray matter3.49e-1034
organ5.87e-10503
telencephalon6.28e-1034
ectoderm-derived structure7.07e-10171
ectoderm7.07e-10171
presumptive ectoderm7.07e-10171
regional part of telencephalon2.12e-0932
cerebral hemisphere2.30e-0932
anatomical conduit3.19e-09240
organism subdivision3.28e-09264
tube5.90e-09192
mesenchyme1.80e-08160
entire embryonic mesenchyme1.80e-08160
liver1.91e-0719
digestive gland1.91e-0719
liver bud1.91e-0719
abdominal segment of trunk3.12e-0760
abdomen3.12e-0760
organ part3.49e-07218
trunk mesenchyme7.23e-07122
cerebral cortex7.37e-0725
pallium7.37e-0725


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)
MA0003.110.8437
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.11.41335
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
MA0048.14.64626
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.12.526
MA0056.10
MA0057.11.28333
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
MA0073.13.33774
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.13.07281
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
MA0105.11.90157
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
MA0139.11.63368
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.569905
MA0146.19.23949
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.14.75973
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.13.14178
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.24.91669
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
TAF1#687243.343046285745290.008005664898701650.0323169309042788



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.