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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:33, 17 September 2013


Full id: C919_Neurons_Neural_parietal_Astrocyte_duodenum_occipital_temporal



Phase1 CAGE Peaks

Hg19::chr17:49124024..49124036,-p10@SPAG9
Hg19::chr2:105467904..105467924,-p1@ENST00000413121
p1@ENST00000443988
p1@ENST00000458253
p1@uc002tck.1
Hg19::chr2:105470562..105470582,+p5@POU3F3
Hg19::chr2:105470599..105470610,+p6@POU3F3
Hg19::chr6:123101428..123101450,+p@chr6:123101428..123101450
+
Hg19::chr6:98264524..98264558,+p@chr6:98264524..98264558
+
Hg19::chr6:99282570..99282591,+p4@POU3F2
Hg19::chr6:99282592..99282616,+p3@POU3F2
Hg19::chr6:99283040..99283063,+p5@POU3F2


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:0021985neurohypophysis development0.00635789657521692
GO:0021979hypothalamus cell differentiation0.00635789657521692
GO:0021854hypothalamus development0.00635789657521692
GO:0014002astrocyte development0.00635789657521692
GO:0021761limbic system development0.00826417063337453
GO:0048708astrocyte differentiation0.00826417063337453
GO:0021983pituitary gland development0.00826417063337453
GO:0040018positive regulation of multicellular organism growth0.00826417063337453
GO:0021536diencephalon development0.00826417063337453
GO:0021782glial cell development0.00826417063337453
GO:0040014regulation of multicellular organism growth0.0108960427314122
GO:0045927positive regulation of growth0.0108960427314122
GO:0035264multicellular organism growth0.0108960427314122
GO:0001669acrosome0.0108960427314122
GO:0050770regulation of axonogenesis0.0110167854537886
GO:0010001glial cell differentiation0.0115194470888124
GO:0035270endocrine system development0.0123365310940337
GO:0042063gliogenesis0.0127094295453305
GO:0050767regulation of neurogenesis0.0127094295453305
GO:0030900forebrain development0.0139182114861477
GO:0048732gland development0.0139182114861477
GO:0007409axonogenesis0.0308770916361527
GO:0048667neuron morphogenesis during differentiation0.0308770916361527
GO:0048812neurite morphogenesis0.0308770916361527
GO:0000904cellular morphogenesis during differentiation0.0308770916361527
GO:0031175neurite development0.0308770916361527
GO:0008544epidermis development0.0308770916361527
GO:0007420brain development0.0308770916361527
GO:0045595regulation of cell differentiation0.0308770916361527
GO:0007398ectoderm development0.0308770916361527
GO:0048666neuron development0.0315146554353818
GO:0005764lysosome0.0335936865800335
GO:0040008regulation of growth0.0335936865800335
GO:0000323lytic vacuole0.0335936865800335
GO:0032990cell part morphogenesis0.0335936865800335
GO:0030030cell projection organization and biogenesis0.0335936865800335
GO:0048858cell projection morphogenesis0.0335936865800335
GO:0030182neuron differentiation0.0335936865800335
GO:0007283spermatogenesis0.0335936865800335
GO:0048232male gamete generation0.0335936865800335
GO:0005773vacuole0.0339849946966792
GO:0008284positive regulation of cell proliferation0.0339849946966792
GO:0007417central nervous system development0.0339849946966792
GO:0050793regulation of developmental process0.0339849946966792
GO:0048699generation of neurons0.0340715777262218
GO:0022008neurogenesis0.0355757701702134
GO:0007276gamete generation0.0355757701702134
GO:0009888tissue development0.040220148346657
GO:0019953sexual reproduction0.040685094257863
GO:0042802identical protein binding0.0460402262403028



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><br>

Cell Type
Ontology termp-valuen
neural cell1.31e-1125
astrocyte of the cerebral cortex2.85e-093
oligodendrocyte3.52e-097
macroglial cell3.52e-097
astrocyte3.52e-097
oligodendrocyte precursor cell3.52e-097
neuronal stem cell5.99e-098
neurectodermal cell7.78e-0759
Uber Anatomy
Ontology termp-valuen
neural tube4.47e-10156
neural rod4.47e-10156
future spinal cord4.47e-10156
neural keel4.47e-10156
central nervous system3.30e-9981
nervous system6.43e-9889
regional part of nervous system1.75e-9453
regional part of brain1.75e-9453
brain2.25e-8068
future brain2.25e-8068
neurectoderm3.67e-7886
regional part of forebrain1.56e-7641
forebrain1.56e-7641
anterior neural tube1.56e-7641
future forebrain1.56e-7641
telencephalon3.60e-7434
neural plate9.47e-7482
presumptive neural plate9.47e-7482
brain grey matter1.74e-7334
gray matter1.74e-7334
cerebral hemisphere2.22e-6932
regional part of telencephalon3.96e-6932
ecto-epithelium4.87e-60104
pre-chordal neural plate6.39e-5761
ectoderm-derived structure2.30e-56171
ectoderm2.30e-56171
presumptive ectoderm2.30e-56171
cerebral cortex3.87e-5325
pallium3.87e-5325
regional part of cerebral cortex1.67e-4522
structure with developmental contribution from neural crest3.14e-44132
neocortex5.93e-4120
adult organism1.05e-36114
organ system subdivision2.06e-35223
posterior neural tube2.95e-2415
chordal neural plate2.95e-2415
basal ganglion1.17e-219
nuclear complex of neuraxis1.17e-219
aggregate regional part of brain1.17e-219
collection of basal ganglia1.17e-219
cerebral subcortex1.17e-219
neural nucleus2.71e-219
nucleus of brain2.71e-219
tube3.38e-21192
segmental subdivision of nervous system1.32e-2013
segmental subdivision of hindbrain2.77e-1812
hindbrain2.77e-1812
presumptive hindbrain2.77e-1812
anatomical cluster9.27e-18373
telencephalic nucleus3.81e-177
gyrus1.79e-156
brainstem1.28e-146
anatomical conduit2.40e-14240
temporal lobe2.38e-136
limbic system4.00e-135
parietal lobe4.65e-135
organ part1.59e-12218
regional part of metencephalon5.05e-129
metencephalon5.05e-129
future metencephalon5.05e-129
epithelium8.76e-12306
cell layer1.54e-11309
corpus striatum1.37e-104
striatum1.37e-104
ventral part of telencephalon1.37e-104
future corpus striatum1.37e-104
multi-tissue structure4.44e-09342
occipital lobe7.52e-095
frontal cortex1.27e-083
embryo1.62e-08592
medulla oblongata2.57e-083
myelencephalon2.57e-083
future myelencephalon2.57e-083
caudate-putamen3.65e-083
dorsal striatum3.65e-083
pons5.54e-083
developing anatomical structure6.74e-08581
germ layer8.77e-08560
germ layer / neural crest8.77e-08560
embryonic tissue8.77e-08560
presumptive structure8.77e-08560
germ layer / neural crest derived structure8.77e-08560
epiblast (generic)8.77e-08560
spinal cord9.01e-083
dorsal region element9.01e-083
dorsum9.01e-083
embryonic structure1.31e-07564


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)
MA0003.10.0913842
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.205864
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.11.40203
MA0029.10.785955
MA0030.11.82437
MA0031.11.69202
MA0038.12.20905
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.14.64144
MA0056.10
MA0057.13.14271
MA0058.10.325084
MA0059.10.323879
MA0060.16.35239
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.12.35343
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.16.04985
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.11.01254
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.229733
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.11.50574
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.39929
MA0146.10.319685
MA0147.10.607251
MA0148.11.11902
MA0149.10.464973
MA0062.20.421263
MA0035.20.473658
MA0039.20.679176
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.486672
MA0047.20.542971
MA0112.20.166662
MA0065.20.719797
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.359913
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.13.32001
MA0163.14.4492
MA0164.10.583138
MA0080.20.739941
MA0018.20.556211
MA0099.20.481058
MA0079.212.8507
MA0102.21.41188
MA0258.10.180288
MA0259.10.624802
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
CTBP2#1488213.93711118651740.008492823486205670.0324248580543167
NANOG#7992339.748259493670880.002874553687984370.0155721516997458
SUZ12#23512316.70526030368760.0006093266768462050.00508530196604929



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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