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{{Coexpression_clusters
{
|full_id=C759_nonsmall_gastrointestinal_occipital_pineal_cerebellum_small_argyrophil
|

Latest revision as of 11:30, 17 September 2013


Full id: C759_nonsmall_gastrointestinal_occipital_pineal_cerebellum_small_argyrophil



Phase1 CAGE Peaks

Hg19::chr15:48483855..48483892,+p1@CTXN2
p2@SLC12A1
Hg19::chr18:40857274..40857292,-p5@SYT4
Hg19::chr18:40857296..40857305,-p8@SYT4
Hg19::chr18:40857329..40857357,-p2@SYT4
Hg19::chr18:40857368..40857384,-p6@SYT4
Hg19::chr18:40857389..40857405,-p3@SYT4
Hg19::chr18:40857447..40857461,-p1@SYT4
Hg19::chr18:40857470..40857481,-p7@SYT4
Hg19::chr18:40857484..40857491,-p9@SYT4
Hg19::chr18:40857493..40857505,-p4@SYT4
Hg19::chr6:158957739..158957759,+p3@TMEM181


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

GO IDGO nameFDR corrected p-value
GO:0007269neurotransmitter secretion0.0360628509212003
GO:0045055regulated secretory pathway0.0360628509212003
GO:0048471perinuclear region of cytoplasm0.0360628509212003
GO:0003001generation of a signal involved in cell-cell signaling0.0360628509212003
GO:0008021synaptic vesicle0.0360628509212003
GO:0001505regulation of neurotransmitter levels0.0360628509212003
GO:0043005neuron projection0.0360628509212003
GO:0030136clathrin-coated vesicle0.0447778552108827



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
neuronal stem cell1.91e-118
neuron2.88e-116
neuroblast2.88e-116
electrically signaling cell2.88e-116
Uber Anatomy
Ontology termp-valuen
nervous system3.45e-8689
central nervous system2.23e-8581
neural tube7.41e-8156
neural rod7.41e-8156
future spinal cord7.41e-8156
neural keel7.41e-8156
regional part of nervous system8.21e-7653
regional part of brain8.21e-7653
brain3.48e-6668
future brain3.48e-6668
regional part of forebrain6.22e-6441
forebrain6.22e-6441
anterior neural tube6.22e-6441
future forebrain6.22e-6441
neurectoderm2.69e-5686
neural plate8.68e-5382
presumptive neural plate8.68e-5382
telencephalon1.46e-5034
adult organism1.70e-50114
brain grey matter1.85e-5034
gray matter1.85e-5034
cerebral hemisphere1.04e-4732
regional part of telencephalon4.30e-4732
ectoderm-derived structure2.74e-45171
ectoderm2.74e-45171
presumptive ectoderm2.74e-45171
ecto-epithelium3.80e-42104
pre-chordal neural plate1.56e-4161
regional part of cerebral cortex6.48e-4122
organ system subdivision1.42e-38223
neocortex2.38e-3720
cerebral cortex2.29e-3525
pallium2.29e-3525
structure with developmental contribution from neural crest6.23e-30132
anatomical cluster1.75e-18373
tube6.77e-18192
posterior neural tube2.05e-1715
chordal neural plate2.05e-1715
basal ganglion1.07e-169
nuclear complex of neuraxis1.07e-169
aggregate regional part of brain1.07e-169
collection of basal ganglia1.07e-169
cerebral subcortex1.07e-169
neural nucleus2.07e-169
nucleus of brain2.07e-169
diencephalon1.28e-147
future diencephalon1.28e-147
anatomical conduit2.22e-13240
telencephalic nucleus3.71e-137
gyrus3.91e-136
segmental subdivision of hindbrain6.28e-1312
hindbrain6.28e-1312
presumptive hindbrain6.28e-1312
segmental subdivision of nervous system8.89e-1213
brainstem9.74e-126
occipital lobe3.66e-115
parietal lobe4.07e-115
temporal lobe8.56e-116
limbic system1.34e-105
gland of diencephalon9.13e-104
neuroendocrine gland9.13e-104
organ part6.43e-09218
regional part of diencephalon7.14e-094
corpus striatum7.59e-094
striatum7.59e-094
ventral part of telencephalon7.59e-094
future corpus striatum7.59e-094
embryo1.17e-08592
epithelium1.35e-08306
regional part of metencephalon2.01e-089
metencephalon2.01e-089
future metencephalon2.01e-089
cell layer2.24e-08309
germ layer2.53e-08560
germ layer / neural crest2.53e-08560
embryonic tissue2.53e-08560
presumptive structure2.53e-08560
germ layer / neural crest derived structure2.53e-08560
epiblast (generic)2.53e-08560
embryonic structure4.10e-08564
developing anatomical structure9.82e-08581
frontal cortex1.71e-073
multi-tissue structure2.29e-07342
caudate-putamen5.97e-073
dorsal striatum5.97e-073
pons7.02e-073
Disease
Ontology termp-valuen
neuroectodermal tumor2.80e-1110
neuroendocrine tumor3.21e-086


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)
MA0003.10.0768054
MA0004.10.349539
MA0006.10.605586
MA0007.10.332734
MA0009.10.79061
MA0014.11.06611
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.15.12606
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.185335
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.13.78104
MA0056.10
MA0057.13.86138
MA0058.10.265212
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.19.86287
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.140284
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.11.96756
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.12.33914
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.11.11087
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.153042
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.11.84316
MA0141.10.2626
MA0142.10.602852
MA0143.10.498176
MA0144.10.142196
MA0145.10.822953
MA0146.10.00165539
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.21.84093
MA0039.20.166893
MA0138.23.34637
MA0002.20.111226
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.784016
MA0065.20.28513
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.153348
MA0155.10.0230394
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.162854
MA0160.10.386031
MA0161.10
MA0162.10.761942
MA0163.10.232847
MA0164.15.58612
MA0080.20.21336
MA0018.20.483823
MA0099.20.411824
MA0079.26.03814
MA0102.21.32663
MA0258.10.420151
MA0259.10.504687
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

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

TF#promotersEnrichmentp-valueq-value
CTCF#1066494.38566430524321.04204760534736e-050.000270857167383953
RAD21#588598.472300459918813.34431965405885e-082.24039384445319e-06
REST#5978119.650028716128021.47593496597899e-111.80709462968206e-09
SIN3A#2594273.442017553427810.001206753943353430.00818284476625688
TBP#690893.032812380351590.0002388258630576910.00260063959043709
YY1#752873.125290477179730.002193839507732880.0126447243017723
ZNF263#10127107.474401488191526.91943485229632e-095.40103779177112e-07



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.

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