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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.109320656384827,0.055712496781182,0.0972869140252862,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0392295810357272,0,0.0365629421359175,0.0534545700183436,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0428357178336246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.113916282738781,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.40595691901074,0.302135515429148,0.828753238223693,0,0,0,0,0,0,0,0.0713034174053426,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0380513783661453,0,0,0,0,0,0,0,0,0,0,0.0355204411879812,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0440785955756708,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.231303150876184,0,0,0,0,0,0,0.0422874684771159,0,0,0,0,0,0,0,0,0,0.241084245299456,0,0,0,0,0,0,0,0,0,0.0695293501927681,0,0.0938392746630608,0,0.0455495587624001,0.20169617591284,0.219625436886832,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0283276594447047,0,0.0914082188667263,0,0,0,0,0,0.2828980264685,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0884836478019413,0,0,0.0980353512377064,0,0,0,0,0,0,0,0,0,0,0.0553417076709348,0.0432061579680018,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.254120022070344,0.148790834525069,0,0,0,0,0,0.134972693361015,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0528027736253869,0.0539356558948951,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.442814589183038,0.90066732173075,0.243322253338365,0,0.0456863240084368,0.0261639379934246,0,0,0,0,0,0,0.0587755320721174,0,0,0,0,0.0974544165143517,0,0,0,0,0,0,0,0,0,0,0,0,0.140132417719247,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0706617474389824,0,0,0,0,0,0.191180892262599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.121715556368437,0,0.0450136346124787,0,0.0837085814034122,0,0,0,0,0,0,0,0.0524855729980601,0,0.169939272094492,0.208266392091069,0.302825730485225,0.10606470902502,0.257049046425766,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.126354806191501,0.250682963288844,0.150256972842231,0.140034794334561,0.320966228024776,0,0,0,0,0,0,0,0,0,0,0,0.0285589446518912,0.123480492992954,0,0,0,0.0633767449113307,0,0,0,0,0,0.0637136642840507,0,0,0,0,0,0,0,0,0.0355151496094428,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0452997049655463,0,0,0,0,0,0,0.0778431765528363,0,0,0,0,0,0,0,0,0,0,0,0,0,0.169068829801421,0.272468530679021,0,0,0,0,0,0.0450355340939671,0.0518077165209662,0,0,0,0,0,0,0,0.0816590494793475,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C1173_medial_Neurons_parietal_temporal_medulloblastoma_occipital_duodenum|gostat_on_coexpression_clusters=GO:0015701!bicarbonate transport!0.0148344369575556!57282$GO:0005452!inorganic anion exchanger activity!0.0203799424963334!57282$GO:0015380!anion exchanger activity!0.0203799424963334!57282$GO:0015106!bicarbonate transmembrane transporter activity!0.0203799424963334!57282$GO:0015301!anion:anion antiporter activity!0.0203799424963334!57282$GO:0015108!chloride transmembrane transporter activity!0.0203799424963334!57282$GO:0015103!inorganic anion transmembrane transporter activity!0.0295885942881831!57282$GO:0006821!chloride transport!0.0295885942881831!57282$GO:0016021!integral to membrane!0.0295885942881831!57282;196500;2823$GO:0031224!intrinsic to membrane!0.0295885942881831!57282;196500;2823$GO:0015297!antiporter activity!0.0295885942881831!57282$GO:0031402!sodium ion binding!0.0295885942881831!57282$GO:0044425!membrane part!0.03799062177336!57282;196500;2823$GO:0009986!cell surface!0.0390393382816885!2823$GO:0006814!sodium ion transport!0.0425601845010815!57282$GO:0008509!anion transmembrane transporter 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.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.88373,MA0105.1;0.695228,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;1.39213,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;0.186511,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;0.0807715,MA0146.1;0.547931,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;0.128723,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.262665,MA0065.2;0.0828768,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;0.534073,MA0156.1;0.959643,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.106355,MA0163.1;1.30651,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;0.0109305,MA0102.2;1.51913,MA0258.1;0.245543,MA0259.1;0.289405,MA0442.1;0}}
|full_id=C1173_medial_Neurons_parietal_temporal_medulloblastoma_occipital_duodenum
|id=C1173
}}

Latest revision as of 11:39, 17 September 2013


Full id: C1173_medial_Neurons_parietal_temporal_medulloblastoma_occipital_duodenum



Phase1 CAGE Peaks

Hg19::chr12:6804456..6804460,-p13@C12orf53
Hg19::chr1:151040388..151040403,+p@chr1:151040388..151040403
+
Hg19::chr1:151040448..151040470,+p@chr1:151040448..151040470
+
Hg19::chr1:151040524..151040538,+p@chr1:151040524..151040538
+
Hg19::chr2:162280765..162280777,+p6@SLC4A10
Hg19::chr4:176594862..176594876,-p29@GPM6A
Hg19::chr5:73931110..73931127,-p@chr5:73931110..73931127
-


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:0015701bicarbonate transport0.0148344369575556
GO:0005452inorganic anion exchanger activity0.0203799424963334
GO:0015380anion exchanger activity0.0203799424963334
GO:0015106bicarbonate transmembrane transporter activity0.0203799424963334
GO:0015301anion:anion antiporter activity0.0203799424963334
GO:0015108chloride transmembrane transporter activity0.0203799424963334
GO:0015103inorganic anion transmembrane transporter activity0.0295885942881831
GO:0006821chloride transport0.0295885942881831
GO:0016021integral to membrane0.0295885942881831
GO:0031224intrinsic to membrane0.0295885942881831
GO:0015297antiporter activity0.0295885942881831
GO:0031402sodium ion binding0.0295885942881831
GO:0044425membrane part0.03799062177336
GO:0009986cell surface0.0390393382816885
GO:0006814sodium ion transport0.0425601845010815
GO:0008509anion transmembrane transporter activity0.0481199389556421
GO:0031420alkali metal ion binding0.0481199389556421
GO:0015293symporter activity0.049511673759731
GO:0015698inorganic anion transport0.0495876489133867
GO:0016020membrane0.0495876489133867



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
nervous system9.43e-6989
central nervous system5.62e-6881
regional part of nervous system4.30e-6653
regional part of brain4.30e-6653
neural tube9.99e-6656
neural rod9.99e-6656
future spinal cord9.99e-6656
neural keel9.99e-6656
brain5.56e-6468
future brain5.56e-6468
telencephalon3.18e-6134
brain grey matter3.58e-6134
gray matter3.58e-6134
cerebral hemisphere4.98e-6132
cerebral cortex1.36e-5725
pallium1.36e-5725
regional part of forebrain2.08e-5741
forebrain2.08e-5741
anterior neural tube2.08e-5741
future forebrain2.08e-5741
regional part of telencephalon2.38e-5632
regional part of cerebral cortex7.88e-5022
neural plate2.74e-4982
presumptive neural plate2.74e-4982
neurectoderm4.04e-4986
neocortex3.18e-4420
pre-chordal neural plate4.63e-4461
ecto-epithelium9.99e-39104
ectoderm-derived structure1.38e-36171
ectoderm1.38e-36171
presumptive ectoderm1.38e-36171
structure with developmental contribution from neural crest2.30e-28132
organ system subdivision5.66e-24223
adult organism5.56e-21114
gyrus1.06e-186
parietal lobe1.16e-155
tube3.45e-13192
temporal lobe2.54e-116
anatomical cluster2.71e-11373
brainstem6.77e-116
posterior neural tube2.00e-1015
chordal neural plate2.00e-1015
occipital lobe2.80e-105
segmental subdivision of hindbrain3.23e-1012
hindbrain3.23e-1012
presumptive hindbrain3.23e-1012
frontal cortex3.66e-103
limbic system5.27e-105
organ part1.15e-09218
segmental subdivision of nervous system2.35e-0913
anatomical conduit1.10e-08240
pons1.24e-083
middle frontal gyrus1.50e-072
neural nucleus1.51e-079
nucleus of brain1.51e-079
regional part of metencephalon1.70e-079
metencephalon1.70e-079
future metencephalon1.70e-079
middle temporal gyrus1.70e-072
epithelium1.73e-07306
cell layer2.54e-07309
Ammon's horn2.62e-072
lobe parts of cerebral cortex2.62e-072
hippocampal formation2.62e-072
limbic lobe2.62e-072
corpus striatum6.74e-074
striatum6.74e-074
ventral part of telencephalon6.74e-074
future corpus striatum6.74e-074


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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0723474
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.11.8966
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.382278
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.0407081
MA0056.10
MA0057.10.369442
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.575931
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.00958848
MA0074.11.46532
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.252594
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.88373
MA0105.10.695228
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.11.39213
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.186511
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.0807715
MA0146.10.547931
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.128723
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.262665
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.10.534073
MA0156.10.959643
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.11.30651
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.20.0109305
MA0102.21.51913
MA0258.10.245543
MA0259.10.289405
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

This analysis result is provided for C0 - C305 clusters.

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