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{{Coexpression_clusters
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9802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,1.63757,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.99724,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224|tfbs_overrepresentation_jaspar=MA0003.1;1.54338,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;3.90467,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;2.16573,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;3.15662,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.04561,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.990225,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.846801,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;4.65896,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;1.12079,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;2.11725,MA0146.1;2.3244,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.481578,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3840_optic_cerebellum_Neutrophils_Eosinophils_occipital_skeletal_substantia
|gostat_on_coexpression_clusters=GO:0008089!anterograde axon cargo transport!0.00476863299187566!23095$GO:0008088!axon cargo transport!0.00476863299187566!23095$GO:0019894!kinesin binding!0.00476863299187566!23095$GO:0007274!neuromuscular synaptic transmission!0.00476863299187566!23095$GO:0007270!nerve-nerve synaptic transmission!0.00805369127516778!23095$GO:0030659!cytoplasmic vesicle membrane!0.029936418226775!23095$GO:0044433!cytoplasmic vesicle part!0.029936418226775!23095$GO:0012506!vesicle membrane!0.029936418226775!23095$GO:0003777!microtubule motor activity!0.0332038149063935!23095$GO:0007018!microtubule-based movement!0.0346167432002826!23095$GO:0005875!microtubule associated complex!0.0346167432002826!23095$GO:0030705!cytoskeleton-dependent intracellular transport!0.0346167432002826!23095$GO:0007268!synaptic transmission!0.0414458966207465!23095$GO:0005874!microtubule!0.0414458966207465!23095$GO:0007017!microtubule-based process!0.0414458966207465!23095$GO:0019226!transmission of nerve impulse!0.0414458966207465!23095$GO:0016023!cytoplasmic membrane-bound vesicle!0.0414458966207465!23095$GO:0031988!membrane-bound vesicle!0.0414458966207465!23095$GO:0031410!cytoplasmic vesicle!0.0457788767220064!23095$GO:0031982!vesicle!0.0457788767220064!23095
|id=C3840
|ontology_enrichment_celltype=CL:0002057!4.36e-16!42;CL:0000860!7.32e-15!45;CL:0000766!5.03e-14!76;CL:0002009!3.10e-13!65;CL:0002194!1.41e-12!63;CL:0000576!1.41e-12!63;CL:0000040!1.41e-12!63;CL:0000559!1.41e-12!63;CL:0000557!1.25e-11!71;CL:0000839!2.11e-09!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.40e-35!115;UBERON:0001017!6.76e-32!82;UBERON:0001049!1.07e-30!57;UBERON:0005068!1.07e-30!57;UBERON:0006241!1.07e-30!57;UBERON:0007135!1.07e-30!57;UBERON:0005743!2.57e-30!86;UBERON:0000468!7.28e-29!659;UBERON:0000467!9.39e-29!625;UBERON:0000480!1.03e-28!626;UBERON:0000955!3.13e-28!69;UBERON:0006238!3.13e-28!69;UBERON:0000073!5.89e-28!94;UBERON:0001016!5.89e-28!94;UBERON:0002616!1.18e-27!59;UBERON:0003080!1.74e-24!42;UBERON:0002780!3.38e-24!41;UBERON:0001890!3.38e-24!41;UBERON:0006240!3.38e-24!41;UBERON:0000062!4.93e-24!511;UBERON:0003075!1.37e-23!86;UBERON:0007284!1.37e-23!86;UBERON:0000922!3.85e-23!612;UBERON:0002050!3.68e-22!605;UBERON:0005423!3.68e-22!605;UBERON:0000923!9.81e-22!604;UBERON:0005291!9.81e-22!604;UBERON:0006598!9.81e-22!604;UBERON:0002532!9.81e-22!604;UBERON:0000033!1.53e-21!123;UBERON:0002346!2.03e-21!90;UBERON:0001893!1.33e-20!34;UBERON:0002020!1.46e-20!34;UBERON:0003528!1.46e-20!34;UBERON:0002791!5.57e-20!33;UBERON:0000153!9.09e-20!129;UBERON:0007811!9.09e-20!129;UBERON:0004121!2.13e-19!169;UBERON:0001869!3.00e-19!32;UBERON:0000924!3.53e-18!173;UBERON:0006601!3.53e-18!173;UBERON:0003056!1.40e-16!61;UBERON:0000956!3.11e-15!25;UBERON:0000203!3.11e-15!25;UBERON:0002619!2.66e-14!22;UBERON:0001950!4.39e-13!20;UBERON:0004765!4.99e-11!101;UBERON:0001434!4.99e-11!101;UBERON:0004111!9.46e-11!241;UBERON:0001474!1.86e-10!86;UBERON:0002371!1.41e-09!80;UBERON:0000025!1.48e-09!194;UBERON:0000477!1.14e-08!286;UBERON:0000475!7.85e-08!365;UBERON:0003076!1.99e-07!15;UBERON:0003057!1.99e-07!15;UBERON:0002204!5.53e-07!167;UBERON:0000483!5.66e-07!309;UBERON:0000119!7.97e-07!312;UBERON:0002308!8.48e-07!9;UBERON:0000125!8.48e-07!9
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3840_optic_cerebellum_Neutrophils_Eosinophils_occipital_skeletal_substantia



Phase1 CAGE Peaks

Hg19::chr1:10270620..10270637,+p1@KIF1B
Hg19::chr1:10270675..10270686,+p5@KIF1B
Hg19::chr5:147763388..147763474,-p1@ENST00000501695
p1@uc003lpb.1


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:0008089anterograde axon cargo transport0.00476863299187566
GO:0008088axon cargo transport0.00476863299187566
GO:0019894kinesin binding0.00476863299187566
GO:0007274neuromuscular synaptic transmission0.00476863299187566
GO:0007270nerve-nerve synaptic transmission0.00805369127516778
GO:0030659cytoplasmic vesicle membrane0.029936418226775
GO:0044433cytoplasmic vesicle part0.029936418226775
GO:0012506vesicle membrane0.029936418226775
GO:0003777microtubule motor activity0.0332038149063935
GO:0007018microtubule-based movement0.0346167432002826
GO:0005875microtubule associated complex0.0346167432002826
GO:0030705cytoskeleton-dependent intracellular transport0.0346167432002826
GO:0007268synaptic transmission0.0414458966207465
GO:0005874microtubule0.0414458966207465
GO:0007017microtubule-based process0.0414458966207465
GO:0019226transmission of nerve impulse0.0414458966207465
GO:0016023cytoplasmic membrane-bound vesicle0.0414458966207465
GO:0031988membrane-bound vesicle0.0414458966207465
GO:0031410cytoplasmic vesicle0.0457788767220064
GO:0031982vesicle0.0457788767220064



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>

Uber Anatomy
Ontology termp-valuen
adult organism1.51e-35114
central nervous system2.92e-3181
neural tube9.01e-3056
neural rod9.01e-3056
future spinal cord9.01e-3056
neural keel9.01e-3056
nervous system4.91e-2989
regional part of nervous system6.08e-2853
regional part of brain6.08e-2853
brain3.82e-2768
future brain3.82e-2768
multi-cellular organism2.69e-26656
anatomical system4.02e-26624
anatomical group6.66e-26625
regional part of forebrain4.46e-2441
forebrain4.46e-2441
anterior neural tube4.46e-2441
future forebrain4.46e-2441
neural plate1.30e-2282
presumptive neural plate1.30e-2282
embryonic structure5.19e-21564
neurectoderm8.63e-2186
telencephalon1.95e-2034
brain grey matter2.21e-2034
gray matter2.21e-2034
germ layer2.25e-20560
germ layer / neural crest2.25e-20560
embryonic tissue2.25e-20560
presumptive structure2.25e-20560
germ layer / neural crest derived structure2.25e-20560
epiblast (generic)2.25e-20560
structure with developmental contribution from neural crest2.36e-20132
developing anatomical structure3.49e-20581
organ1.08e-19503
embryo1.55e-19592
regional part of telencephalon3.64e-1932
cerebral hemisphere4.44e-1932
ectoderm-derived structure1.70e-17171
ectoderm1.70e-17171
presumptive ectoderm1.70e-17171
pre-chordal neural plate1.43e-1661
organ system subdivision8.01e-16223
ecto-epithelium8.94e-16104
cerebral cortex5.13e-1525
pallium5.13e-1525
regional part of cerebral cortex5.47e-1422
neocortex8.25e-1320
anatomical cluster8.06e-12373
skeletal system1.03e-10100
bone element1.29e-1082
anatomical conduit7.31e-10240
bone marrow1.33e-0976
skeletal element1.91e-0990
tube5.76e-09192
immune system1.04e-0793
multi-tissue structure1.13e-07342
tissue4.70e-07773
hemolymphoid system4.78e-07108
posterior neural tube5.34e-0715
chordal neural plate5.34e-0715
hematopoietic system5.67e-0798
blood island5.67e-0798
basal ganglion7.22e-079
nuclear complex of neuraxis7.22e-079
aggregate regional part of brain7.22e-079
collection of basal ganglia7.22e-079
cerebral subcortex7.22e-079
neural nucleus7.65e-079
nucleus of brain7.65e-079


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.12.16573
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.13.15662
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.990225
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.14.65896
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#1066435.360256373075030.0064925092527670.0279467161459726
CTCFL#140690319.74647435897440.0001298372005551160.00171755128420213
E2F1#186934.907389214879320.008460985347239390.0325412207210582
E2F6#187635.017155731697390.00791769806886330.0322233835482041
ELF1#199734.258097958807540.01295179875054610.0462357434272725
FOS#235338.99795530889440.001372499272417130.00897573271834518
GABPB1#255337.067683836182170.002832212825417420.0154123319754987
IRF1#365937.63716375356390.002244692747297240.0128091719940431
IRF3#3661231.32130147432640.001339514673320110.00887731283500726
MYC#460935.22228187160940.007020843755740150.0294537015868948
NANOG#79923219.49651898734180.003427255648501020.0174468294342853
NFKB1#479035.488063424193840.006049381815655430.0269639105221816
NFYA#4800212.28372046655370.008516011403724430.0324789554116848
NFYB#4801211.17319550235760.01025467135054530.0381351524419455
PAX5#507936.669565531177830.003370290999677260.0172925483525077
PBX3#5090214.60967512449610.006056122473217890.0268359020314991
RAD21#5885310.35503389545630.0009004912073565420.00664075704032692
SIN3A#2594235.408884726815140.006318961977991520.0276788185219753
SMARCB1#6598212.16847718743830.008675002221921740.0329889512472795
SMC3#9126210.02995522995520.0126656379767470.0457474170725741
SP2#6668217.43568699589640.004273568481769740.0203199280067175
TAF7#6879311.43306940492390.0006690181981945830.00543113809570494
YY1#752834.911170749853860.008441455341808260.0329416416112959
ZBTB7A#5134137.35190930787590.002516255860282270.0140202329167744
ZNF263#1012738.221841637010680.001799043925565870.0109416694934879



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3840&oldid=3070957"