Personal tools

Coexpression cluster:C2192

From FANTOM5_SSTAR

Jump to: navigation, search


Full id: C2192_small_signet_gastric_adenocarcinoma_colon_bile_duodenum



Phase1 CAGE Peaks

  Short description
Hg19::chr12:12223867..12223883,+ p1@BCL2L14
Hg19::chr2:241544820..241544829,+ p6@GPR35
Hg19::chr2:241544834..241544861,+ p2@GPR35
Hg19::chr2:241544866..241544882,+ p4@GPR35


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


uberon_data


Uber Anatomy
Ontology termp-valuen
neural tube8.89e-3556
neural rod8.89e-3556
future spinal cord8.89e-3556
neural keel8.89e-3556
adult organism7.15e-33114
regional part of nervous system3.07e-3253
regional part of brain3.07e-3253
organ system subdivision8.77e-30223
brain1.43e-2468
future brain1.43e-2468
brain grey matter3.77e-2334
gray matter3.77e-2334
telencephalon4.76e-2334
gastrointestinal system7.19e-2325
regional part of forebrain1.21e-2241
forebrain1.21e-2241
anterior neural tube1.21e-2241
future forebrain1.21e-2241
central nervous system1.71e-2281
neural plate5.22e-2182
presumptive neural plate5.22e-2182
regional part of telencephalon4.74e-2032
cerebral hemisphere7.31e-2032
neurectoderm1.24e-1986
intestine2.07e-1917
nervous system2.15e-1989
regional part of cerebral cortex6.11e-1922
neocortex3.65e-1820
cerebral cortex2.57e-1625
pallium2.57e-1625
anatomical cluster8.29e-16373
multi-tissue structure1.07e-15342
ecto-epithelium8.90e-15104
tube1.10e-13192
brainstem1.63e-136
posterior neural tube1.75e-1315
chordal neural plate1.75e-1315
pre-chordal neural plate2.27e-1361
subdivision of digestive tract1.64e-12118
large intestine2.61e-1111
segmental subdivision of hindbrain4.91e-1112
hindbrain4.91e-1112
presumptive hindbrain4.91e-1112
anatomical conduit7.14e-11240
structure with developmental contribution from neural crest7.81e-11132
digestive system2.53e-10145
digestive tract2.53e-10145
primitive gut2.53e-10145
segmental subdivision of nervous system4.45e-1013
organ part1.67e-09218
gyrus3.33e-096
small intestine3.65e-094
organ4.00e-09503
lower digestive tract7.21e-095
endoderm-derived structure1.39e-08160
endoderm1.39e-08160
presumptive endoderm1.39e-08160
neural nucleus2.27e-089
nucleus of brain2.27e-089
temporal lobe2.48e-086
medulla oblongata7.08e-083
myelencephalon7.08e-083
future myelencephalon7.08e-083
ectoderm-derived structure1.14e-07171
ectoderm1.14e-07171
presumptive ectoderm1.14e-07171
colon2.20e-079
pons2.62e-073
biliary system6.58e-079
biliary tree6.58e-079
biliary bud6.58e-079


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0055.12.526
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.12.95284
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
MA0145.11.08195
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.13.0262
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.22.1393
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
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
HNF4A#3172317.34921777221530.0003125641557482750.0032142465401924
HNF4G#3174321.56506689483510.0001638032421292610.00203563146177271



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.