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Coexpression cluster:C636: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;4.33156,MA0004.1;2.12862,MA0006.1;5.26661,MA0007.1;0.7221,MA0009.1;0.695988,MA0014.1;1.10943,MA0017.1;0.181071,MA0019.1;1.83523,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;3.69659,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;0.543644,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;0.291389,MA0042.1;0.264992,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;5.74127,MA0050.1;0.73369,MA0051.1;0.359609,MA0052.1;1.51148,MA0055.1;0.00349085,MA0056.1;0,MA0057.1;0.769632,MA0058.1;2.44274,MA0059.1;2.43567,MA0060.1;0.0773489,MA0061.1;0.0626878,MA0063.1;0,MA0066.1;0.363668,MA0067.1;1.00375,MA0068.1;0.169955,MA0069.1;0.681911,MA0070.1;0.671241,MA0071.1;0.329767,MA0072.1;0.666958,MA0073.1;0.0596341,MA0074.1;0.358953,MA0076.1;2.52985,MA0077.1;0.65962,MA0078.1;0.447828,MA0081.1;0.199203,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;1.425,MA0089.1;0,MA0090.1;0.635809,MA0091.1;0.278153,MA0092.1;0.247341,MA0093.1;2.81524,MA0095.1;0,MA0098.1;0,MA0100.1;0.375452,MA0101.1;0.1571,MA0103.1;0.878771,MA0105.1;0.0899037,MA0106.1;1.0329,MA0107.1;0.107387,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.234271,MA0113.1;1.06479,MA0114.1;0.339925,MA0115.1;0.929032,MA0116.1;0.10959,MA0117.1;0.732,MA0119.1;1.04663,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;1.68528,MA0140.1;0.327488,MA0141.1;0.197753,MA0142.1;0.514195,MA0143.1;0.414436,MA0144.1;0.0953756,MA0145.1;4.66763,MA0146.1;0.000361686,MA0147.1;9.14452,MA0148.1;0.296708,MA0149.1;0.319221,MA0062.2;0.473181,MA0035.2;0.326883,MA0039.2;0.839657,MA0138.2;0.44894,MA0002.2;0.0708857,MA0137.2;0.168782,MA0104.2;8.95953,MA0047.2;0.388882,MA0112.2;0.0113102,MA0065.2;0.16797,MA0150.1;0.218956,MA0151.1;0,MA0152.1;0.333125,MA0153.1;0.790794,MA0154.1;0.0872435,MA0155.1;0.0101184,MA0156.1;0.170442,MA0157.1;0.489002,MA0158.1;0,MA0159.1;0.112236,MA0160.1;0.30953,MA0161.1;0,MA0162.1;3.47538,MA0163.1;0.000620686,MA0164.1;0.425415,MA0080.2;0.46983,MA0018.2;0.400879,MA0099.2;0.333432,MA0079.2;0.711847,MA0102.2;1.22472,MA0258.1;0.089643,MA0259.1;1.2329,MA0442.1;0
}}
}}

Revision as of 19:20, 22 January 2013


Full id: C636_thymus_skeletal_cerebellum_Hodgkin_temporal_duodenum_parietal



Phase1 CAGE Peaks

Hg19::chr3:35680783..35680788,+p29@ARPP21
Hg19::chr3:35680971..35680982,+p12@ARPP21
Hg19::chr3:35681007..35681023,+p2@ARPP21
Hg19::chr3:35681084..35681099,+p10@ARPP21
Hg19::chr3:35681110..35681124,+p14@ARPP21
Hg19::chr3:35681137..35681148,+p8@ARPP21
Hg19::chr3:35681164..35681173,+p13@ARPP21
Hg19::chr3:35681192..35681203,+p9@ARPP21
Hg19::chr3:35681221..35681234,+p5@ARPP21
Hg19::chr3:35681260..35681273,+p6@ARPP21
Hg19::chr3:35681346..35681369,+p11@ARPP21
Hg19::chr3:35683726..35683735,+p41@ARPP21
Hg19::chr3:35683816..35683839,+p7@ARPP21
Hg19::chr7:71802595..71802610,-p15@CALN1


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

No GOStat results

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
cell of skeletal muscle4.45e-079
Uber Anatomy
Ontology termp-valuen
neural tube6.33e-6456
neural rod6.33e-6456
future spinal cord6.33e-6456
neural keel6.33e-6456
central nervous system2.54e-6381
regional part of nervous system6.29e-5953
regional part of brain6.29e-5953
nervous system9.47e-5889
telencephalon7.28e-5434
brain grey matter1.04e-5334
gray matter1.04e-5334
brain2.60e-5268
future brain2.60e-5268
cerebral hemisphere1.02e-5032
regional part of telencephalon3.01e-5032
regional part of forebrain3.03e-4941
forebrain3.03e-4941
anterior neural tube3.03e-4941
future forebrain3.03e-4941
neurectoderm3.91e-4786
adult organism1.49e-46114
neural plate1.25e-4582
presumptive neural plate1.25e-4582
regional part of cerebral cortex8.96e-4422
neocortex4.77e-4020
cerebral cortex6.75e-3825
pallium6.75e-3825
pre-chordal neural plate5.32e-3661
ecto-epithelium9.69e-35104
ectoderm-derived structure8.63e-33171
ectoderm8.63e-33171
presumptive ectoderm8.63e-33171
structure with developmental contribution from neural crest5.57e-30132
organ system subdivision1.29e-22223
basal ganglion1.30e-179
nuclear complex of neuraxis1.30e-179
aggregate regional part of brain1.30e-179
collection of basal ganglia1.30e-179
cerebral subcortex1.30e-179
neural nucleus4.58e-179
nucleus of brain4.58e-179
posterior neural tube3.00e-1515
chordal neural plate3.00e-1515
gyrus7.91e-146
telencephalic nucleus9.67e-147
tube3.73e-12192
epithelium5.01e-12306
occipital lobe8.10e-125
cell layer9.33e-12309
temporal lobe1.06e-116
parietal lobe1.08e-115
limbic system3.69e-115
anatomical cluster6.37e-11373
segmental subdivision of hindbrain8.83e-1112
hindbrain8.83e-1112
presumptive hindbrain8.83e-1112
multi-tissue structure2.71e-10342
organ part5.08e-10218
segmental subdivision of nervous system7.95e-1013
corpus striatum5.69e-094
striatum5.69e-094
ventral part of telencephalon5.69e-094
future corpus striatum5.69e-094
regional part of metencephalon9.73e-099
metencephalon9.73e-099
future metencephalon9.73e-099
brainstem1.04e-086
anatomical conduit1.39e-08240
frontal cortex6.43e-083
pons4.47e-073
caudate-putamen5.17e-073
dorsal striatum5.17e-073


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)
MA0003.14.33156
MA0004.12.12862
MA0006.15.26661
MA0007.10.7221
MA0009.10.695988
MA0014.11.10943
MA0017.10.181071
MA0019.11.83523
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.13.69659
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.15.74127
MA0050.10.73369
MA0051.10.359609
MA0052.11.51148
MA0055.10.00349085
MA0056.10
MA0057.10.769632
MA0058.12.44274
MA0059.12.43567
MA0060.10.0773489
MA0061.10.0626878
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.169955
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.0596341
MA0074.10.358953
MA0076.12.52985
MA0077.10.65962
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.11.425
MA0089.10
MA0090.10.635809
MA0091.10.278153
MA0092.10.247341
MA0093.12.81524
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.878771
MA0105.10.0899037
MA0106.11.0329
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.11.06479
MA0114.10.339925
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.11.04663
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.11.68528
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.10.0953756
MA0145.14.66763
MA0146.10.000361686
MA0147.19.14452
MA0148.10.296708
MA0149.10.319221
MA0062.20.473181
MA0035.20.326883
MA0039.20.839657
MA0138.20.44894
MA0002.20.0708857
MA0137.20.168782
MA0104.28.95953
MA0047.20.388882
MA0112.20.0113102
MA0065.20.16797
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.0872435
MA0155.10.0101184
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.13.47538
MA0163.10.000620686
MA0164.10.425415
MA0080.20.46983
MA0018.20.400879
MA0099.20.333432
MA0079.20.711847
MA0102.21.22472
MA0258.10.089643
MA0259.11.2329
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
SUZ12#23512310.73909590951350.002450333088738650.0137919880061857
ZNF263#10127105.87274402643624.43453169106043e-072.11285609161798e-05



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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