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

Latest revision as of 11:08, 17 September 2013


Full id: C261_locus_medial_parietal_pons_diencephalon_olfactory_spinal



Phase1 CAGE Peaks

Hg19::chr16:90002390..90002426,+p@chr16:90002390..90002426
+
Hg19::chr22:29881751..29881764,+p@chr22:29881751..29881764
+
Hg19::chr22:29884834..29884866,+p2@NEFH
Hg19::chr22:29885906..29885916,+p@chr22:29885906..29885916
+
Hg19::chr22:29885940..29885952,+p@chr22:29885940..29885952
+
Hg19::chr22:29885961..29885977,+p@chr22:29885961..29885977
+
Hg19::chr22:29885978..29885988,+p@chr22:29885978..29885988
+
Hg19::chr22:29886000..29886013,+p@chr22:29886000..29886013
+
Hg19::chr22:29886019..29886032,+p@chr22:29886019..29886032
+
Hg19::chr22:29886121..29886139,+p@chr22:29886121..29886139
+
Hg19::chr22:29886313..29886336,+p@chr22:29886313..29886336
+
Hg19::chr2:55254171..55254186,-p30@RTN4
Hg19::chr4:83551018..83551029,-p@chr4:83551018..83551029
-
Hg19::chr5:71503612..71503615,+p4@BC047027
Hg19::chr7:75956472..75956483,-p@chr7:75956472..75956483
-
Hg19::chr8:24773123..24773130,+p18@NEFM
Hg19::chr8:24773140..24773144,+p20@NEFM
Hg19::chr8:24773147..24773196,+p5@NEFM
Hg19::chr8:24773203..24773219,+p16@NEFM
Hg19::chr8:24774582..24774597,+p7@NEFM
Hg19::chr8:24774600..24774620,+p11@NEFM
Hg19::chr8:24774622..24774647,+p2@NEFM
Hg19::chr8:24774653..24774683,+p9@NEFM
Hg19::chr8:24774685..24774698,+p8@NEFM
Hg19::chr8:24774703..24774742,+p6@NEFM
Hg19::chr8:24774749..24774825,+p3@NEFM
Hg19::chr8:24774877..24774889,+p14@NEFM
Hg19::chr8:24774895..24774913,+p13@NEFM
Hg19::chr8:24774940..24775005,-p@chr8:24774940..24775005
-
Hg19::chr8:24774987..24775001,+p4@NEFM
Hg19::chr8:24775132..24775141,+p15@NEFM
Hg19::chr8:24775143..24775154,+p10@NEFM
Hg19::chr8:24775348..24775355,+p@chr8:24775348..24775355
+
Hg19::chr8:24775362..24775367,+p@chr8:24775362..24775367
+
Hg19::chr8:24775373..24775396,+p@chr8:24775373..24775396
+
Hg19::chr8:24775416..24775425,+p@chr8:24775416..24775425
+
Hg19::chr8:24775454..24775468,+p@chr8:24775454..24775468
+
Hg19::chr8:24775490..24775500,+p@chr8:24775490..24775500
+
Hg19::chr8:24775577..24775615,+p@chr8:24775577..24775615
+
Hg19::chr8:24775648..24775668,+p@chr8:24775648..24775668
+
Hg19::chr8:24775682..24775722,-p@chr8:24775682..24775722
-
Hg19::chr8:24775719..24775743,+p@chr8:24775719..24775743
+
Hg19::chr8:24775725..24775777,-p@chr8:24775725..24775777
-
Hg19::chr8:24775779..24775824,-p@chr8:24775779..24775824
-
Hg19::chr8:24810011..24810022,-p3@NEFL
Hg19::chr8:24810368..24810434,+p1@CU691685
Hg19::chr8:24811145..24811158,-p@chr8:24811145..24811158
-
Hg19::chr8:24811170..24811225,-p@chr8:24811170..24811225
-
Hg19::chr8:24811241..24811267,-p@chr8:24811241..24811267
-
Hg19::chr8:24811284..24811297,-p@chr8:24811284..24811297
-
Hg19::chrX:49044292..49044308,-p@chrX:49044292..49044308
-


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

p.valueFDRnGenesnPathwayName
2.4140612493822e-081.52810077085894e-05353Amyotrophic lateral sclerosis (ALS) (KEGG):05014



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:0060053neurofilament cytoskeleton4.23101610269649e-09
GO:0005883neurofilament4.23101610269649e-09
GO:0030424axon4.81680398255976e-07
GO:0045110intermediate filament bundle assembly6.84538130668057e-07
GO:0043005neuron projection3.91095559129903e-06
GO:0060052neurofilament cytoskeleton organization and biogenesis3.91095559129903e-06
GO:0045109intermediate filament organization3.91095559129903e-06
GO:0008088axon cargo transport9.580148792241e-06
GO:0031175neurite development1.07113664769344e-05
GO:0048666neuron development1.38193985235911e-05
GO:0007399nervous system development1.38193985235911e-05
GO:0045104intermediate filament cytoskeleton organization and biogenesis2.07496567459559e-05
GO:0045103intermediate filament-based process2.08846379961956e-05
GO:0032990cell part morphogenesis2.08846379961956e-05
GO:0048858cell projection morphogenesis2.08846379961956e-05
GO:0030030cell projection organization and biogenesis2.08846379961956e-05
GO:0030182neuron differentiation2.14453827583458e-05
GO:0044430cytoskeletal part2.27522652460715e-05
GO:0005882intermediate filament2.5883240202762e-05
GO:0045111intermediate filament cytoskeleton2.5883240202762e-05
GO:0048699generation of neurons2.65804079784278e-05
GO:0022008neurogenesis3.2199136132167e-05
GO:0050770regulation of axonogenesis3.86366421737609e-05
GO:0042995cell projection4.92236542123348e-05
GO:0007017microtubule-based process4.92236542123348e-05
GO:0050767regulation of neurogenesis7.38786335274999e-05
GO:0005856cytoskeleton8.52699397135336e-05
GO:0048731system development0.000133838498078037
GO:0044446intracellular organelle part0.000133838498078037
GO:0044422organelle part0.000133838498078037
GO:0000902cell morphogenesis0.000133838498078037
GO:0032989cellular structure morphogenesis0.000133838498078037
GO:0048856anatomical structure development0.000275992745606819
GO:0005200structural constituent of cytoskeleton0.000286103611385618
GO:0007010cytoskeleton organization and biogenesis0.000359040506163476
GO:0000226microtubule cytoskeleton organization and biogenesis0.000389482381163675
GO:0007275multicellular organismal development0.000422578373894008
GO:0007409axonogenesis0.000461063935069976
GO:0048667neuron morphogenesis during differentiation0.00048537342180161
GO:0048812neurite morphogenesis0.00048537342180161
GO:0000904cellular morphogenesis during differentiation0.000522096502794062
GO:0008090retrograde axon cargo transport0.000528510109930102
GO:0033693neurofilament bundle assembly0.000528510109930102
GO:0033596TSC1-TSC2 complex0.000528510109930102
GO:0043232intracellular non-membrane-bound organelle0.00087136633023563
GO:0043228non-membrane-bound organelle0.00087136633023563
GO:0007018microtubule-based movement0.00091716122221323
GO:0009653anatomical structure morphogenesis0.00091716122221323
GO:0031133regulation of axon diameter0.000930123030426531
GO:0019896axon transport of mitochondrion0.000930123030426531
GO:0030705cytoskeleton-dependent intracellular transport0.00101433288656327
GO:0016043cellular component organization and biogenesis0.00121196012980163
GO:0032502developmental process0.00126827491445492
GO:0019987negative regulation of anti-apoptosis0.00126827491445492
GO:0030517negative regulation of axon extension0.00126827491445492
GO:0048468cell development0.00130133684677868
GO:0050793regulation of developmental process0.00131382944009915
GO:0032501multicellular organismal process0.00197025161148262
GO:0008089anterograde axon cargo transport0.00197025161148262
GO:0006996organelle organization and biogenesis0.00222492379745686
GO:0031594neuromuscular junction0.00224976776725475
GO:0050771negative regulation of axonogenesis0.00224976776725475
GO:0001578microtubule bundle formation0.00258291462092895
GO:0048869cellular developmental process0.00338391799232485
GO:0030154cell differentiation0.00338391799232485
GO:0050768negative regulation of neurogenesis0.00404163294447627
GO:0016358dendrite development0.00404163294447627
GO:0045767regulation of anti-apoptosis0.00404163294447627
GO:0030516regulation of axon extension0.00404163294447627
GO:0048675axon extension0.00564219054121416
GO:0005829cytosol0.00600575663579328
GO:0043229intracellular organelle0.00681287527294214
GO:0043226organelle0.00681287527294214
GO:0007026negative regulation of microtubule depolymerization0.00681287527294214
GO:0031114regulation of microtubule depolymerization0.00681287527294214
GO:0031111negative regulation of microtubule polymerization or depolymerization0.00693714164661611
GO:0007019microtubule depolymerization0.00693714164661611
GO:0031110regulation of microtubule polymerization or depolymerization0.00863164222565041
GO:0031109microtubule polymerization or depolymerization0.00940234569647014
GO:0022607cellular component assembly0.0107676993146376
GO:0051261protein depolymerization0.013087176159772
GO:0046907intracellular transport0.013087176159772
GO:0051129negative regulation of cellular component organization and biogenesis0.0145253696570421
GO:0030176integral to endoplasmic reticulum membrane0.0146275959853866
GO:0044424intracellular part0.0150008238923059
GO:0030334regulation of cell migration0.016167772421178
GO:0031227intrinsic to endoplasmic reticulum membrane0.0162473449589946
GO:0051649establishment of cellular localization0.0175591055910402
GO:0051270regulation of cell motility0.0179566926436438
GO:0051641cellular localization0.0180258923310935
GO:0048523negative regulation of cellular process0.0181232143219493
GO:0040012regulation of locomotion0.0181232143219493
GO:0040011locomotion0.0181762756204863
GO:0008022protein C-terminus binding0.0182281790107758
GO:0048519negative regulation of biological process0.018568730079944
GO:0051093negative regulation of developmental process0.018568730079944
GO:0051128regulation of cellular component organization and biogenesis0.0238343265402459
GO:0051248negative regulation of protein metabolic process0.0245289866141991
GO:0005622intracellular0.0259452798575701
GO:0051179localization0.0294502339281616
GO:0044444cytoplasmic part0.0312111074793519
GO:0031301integral to organelle membrane0.0314334501173939
GO:0031300intrinsic to organelle membrane0.0340135051096874
GO:0006916anti-apoptosis0.0376357318201396
GO:0005875microtubule associated complex0.0394468473645381
GO:0044445cytosolic part0.0412212483758672
GO:0005635nuclear envelope0.0416858902861601
GO:0043066negative regulation of apoptosis0.0482313546818419
GO:0043069negative regulation of programmed cell death0.0484118847156383
GO:0016477cell migration0.0485889128549148



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
Merkel cell5.10e-072
Uber Anatomy
Ontology termp-valuen
neural tube1.15e-10856
neural rod1.15e-10856
future spinal cord1.15e-10856
neural keel1.15e-10856
regional part of nervous system7.46e-10053
regional part of brain7.46e-10053
brain6.37e-8668
future brain6.37e-8668
regional part of forebrain2.02e-8541
forebrain2.02e-8541
anterior neural tube2.02e-8541
future forebrain2.02e-8541
central nervous system7.72e-8581
nervous system1.47e-8189
brain grey matter1.20e-7634
gray matter1.20e-7634
telencephalon8.26e-7634
neural plate5.92e-7482
presumptive neural plate5.92e-7482
cerebral hemisphere6.11e-7132
regional part of telencephalon1.50e-7032
neurectoderm5.50e-7086
ecto-epithelium2.48e-61104
regional part of cerebral cortex3.41e-6022
pre-chordal neural plate8.42e-5861
neocortex3.10e-5420
cerebral cortex1.62e-5225
pallium1.62e-5225
adult organism2.11e-50114
structure with developmental contribution from neural crest9.92e-44132
ectoderm-derived structure2.69e-42171
ectoderm2.69e-42171
presumptive ectoderm2.69e-42171
organ system subdivision2.06e-29223
neural nucleus2.62e-259
nucleus of brain2.62e-259
basal ganglion6.12e-259
nuclear complex of neuraxis6.12e-259
aggregate regional part of brain6.12e-259
collection of basal ganglia6.12e-259
cerebral subcortex6.12e-259
tube7.20e-25192
posterior neural tube3.33e-2315
chordal neural plate3.33e-2315
telencephalic nucleus2.53e-197
gyrus2.77e-196
brainstem3.34e-196
anatomical conduit1.59e-17240
parietal lobe9.40e-165
temporal lobe9.53e-166
limbic system1.16e-155
segmental subdivision of hindbrain1.50e-1512
hindbrain1.50e-1512
presumptive hindbrain1.50e-1512
occipital lobe4.35e-155
segmental subdivision of nervous system3.07e-1413
epithelium1.27e-13306
cell layer2.26e-13309
anatomical cluster3.73e-13373
regional part of diencephalon1.15e-124
organ part4.59e-12218
corpus striatum6.23e-124
striatum6.23e-124
ventral part of telencephalon6.23e-124
future corpus striatum6.23e-124
diencephalon4.87e-117
future diencephalon4.87e-117
pons8.50e-113
frontal cortex2.54e-103
spinal cord3.26e-103
dorsal region element3.26e-103
dorsum3.26e-103
medulla oblongata3.91e-103
myelencephalon3.91e-103
future myelencephalon3.91e-103
caudate-putamen1.86e-093
dorsal striatum1.86e-093
multi-tissue structure9.39e-09342
regional part of metencephalon1.57e-089
metencephalon1.57e-089
future metencephalon1.57e-089
organ5.02e-08503
middle frontal gyrus9.83e-082
middle temporal gyrus1.02e-072
locus ceruleus1.02e-072
brainstem nucleus1.02e-072
hindbrain nucleus1.02e-072
Ammon's horn1.49e-072
lobe parts of cerebral cortex1.49e-072
hippocampal formation1.49e-072
limbic lobe1.49e-072
embryo2.41e-07592
amygdala2.53e-072
pineal body2.77e-072
regional part of epithalamus2.77e-072
secretory circumventricular organ2.77e-072
circumventricular organ2.77e-072
epithalamus2.77e-072
dorsal plus ventral thalamus4.81e-072


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)
MA0003.15.78061e-12
MA0004.10.0287532
MA0006.10.0290142
MA0007.10.024623
MA0009.10.252434
MA0014.11.14887e-11
MA0017.10.00870385
MA0019.10.0757474
MA0024.10.183969
MA0025.12.4963
MA0027.11.73105
MA0028.10.0348968
MA0029.11.08244
MA0030.10.188804
MA0031.10.150659
MA0038.10.213125
MA0040.10.199633
MA0041.10.0332488
MA0042.10.264815
MA0043.10.252653
MA0046.10.685727
MA0048.10.00351449
MA0050.10.109642
MA0051.10.0572096
MA0052.10.202085
MA0055.11.0756
MA0056.10
MA0057.10.0812865
MA0058.10.0568651
MA0059.10.0561949
MA0060.10.000588275
MA0061.10.0687895
MA0063.10
MA0066.11.23063
MA0067.10.49981
MA0068.18.92408e-05
MA0069.10.242306
MA0070.10.234718
MA0071.10.0459331
MA0072.10.231695
MA0073.11.15334e-13
MA0074.10.0569489
MA0076.10.0138475
MA0077.10.226543
MA0078.10.321356
MA0081.17.9135
MA0083.10.25765
MA0084.10.664025
MA0087.10.230056
MA0088.10.00767257
MA0089.10
MA0090.10.191226
MA0091.10.289788
MA0092.11.4496
MA0093.10.0300741
MA0095.10
MA0098.10
MA0100.10.227752
MA0101.10.200267
MA0103.10.318689
MA0105.10.00563636
MA0106.10.0741862
MA0107.10.496379
MA0108.20.14894
MA0109.10
MA0111.10.082444
MA0113.10.0808928
MA0114.10.179021
MA0115.10.436009
MA0116.10.729675
MA0117.10.27892
MA0119.10.274103
MA0122.10.297683
MA0124.11.03875
MA0125.10.336564
MA0130.10
MA0131.10.10574
MA0132.10
MA0133.10
MA0135.10.27375
MA0136.11.25703
MA0139.10.000203372
MA0140.10.389168
MA0141.10.0552982
MA0142.10.133251
MA0143.10.582117
MA0144.12.10189
MA0145.11.47713e-05
MA0146.19.46233e-10
MA0147.10.00196312
MA0148.10.0348816
MA0149.10.0422402
MA0062.20.122451
MA0035.20.171459
MA0039.22.7447e-11
MA0138.20.0978028
MA0002.20.00348218
MA0137.20.905104
MA0104.20.0005775
MA0047.20.0694194
MA0112.27.01122e-07
MA0065.20.206774
MA0150.10.0151269
MA0151.10
MA0152.12.05334
MA0153.10.865299
MA0154.11.15244
MA0155.10.0317588
MA0156.10.408437
MA0157.10.119034
MA0158.10
MA0159.10.00198615
MA0160.10.152819
MA0161.10
MA0162.17.17851e-09
MA0163.10.000201516
MA0164.13.3867
MA0080.25.41959
MA0018.20.0747401
MA0099.20.0472524
MA0079.21.90069e-13
MA0102.20.697711
MA0258.10.0254544
MA0259.10.0144768
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

No analysis results for this cluster

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

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