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Coexpression cluster:C1878: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;1.80249,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;3.07977,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.603517,MA0056.1;0,MA0057.1;0.554727,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.215829,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.412364,MA0089.1;0,MA0090.1;2.34702,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;1.58771,MA0106.1;0.779931,MA0107.1;0.985964,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;4.34317,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.759606,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;2.01656,MA0146.1;0.6031,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;1.63245,MA0062.2;1.41923,MA0035.2;0.691506,MA0039.2;0.527987,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.449243,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.98952,MA0155.1;1.91168,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.21472,MA0163.1;1.99104,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.146371,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:15, 22 January 2013


Full id: C1878_thyroid_aorta_temporal_occipital_throat_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr2:107502615..107502628,-p5@ST6GAL2
Hg19::chr2:107503290..107503348,-p1@ST6GAL2
Hg19::chr2:107503558..107503580,-p8@ST6GAL2
Hg19::chr2:107503727..107503742,-p4@ST6GAL2
Hg19::chr2:107503767..107503775,-p13@ST6GAL2


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
central nervous system3.98e-4481
neural tube2.13e-4156
neural rod2.13e-4156
future spinal cord2.13e-4156
neural keel2.13e-4156
nervous system2.28e-4189
regional part of nervous system1.14e-3953
regional part of brain1.14e-3953
brain3.52e-3668
future brain3.52e-3668
telencephalon1.27e-3334
brain grey matter1.54e-3334
gray matter1.54e-3334
adult organism4.37e-33114
regional part of forebrain5.40e-3341
forebrain5.40e-3341
anterior neural tube5.40e-3341
future forebrain5.40e-3341
cerebral hemisphere2.92e-3132
regional part of telencephalon6.99e-3132
neurectoderm9.94e-3186
neural plate8.93e-3082
presumptive neural plate8.93e-3082
regional part of cerebral cortex1.32e-2422
ecto-epithelium3.26e-24104
organ system subdivision8.15e-24223
ectoderm-derived structure2.83e-23171
ectoderm2.83e-23171
presumptive ectoderm2.83e-23171
pre-chordal neural plate4.67e-2361
cerebral cortex5.47e-2325
pallium5.47e-2325
neocortex6.95e-2220
structure with developmental contribution from neural crest1.06e-21132
anatomical cluster1.32e-14373
tube3.13e-14192
neural nucleus4.14e-129
nucleus of brain4.14e-129
multi-tissue structure1.18e-10342
anatomical conduit1.45e-09240
basal ganglion1.46e-099
nuclear complex of neuraxis1.46e-099
aggregate regional part of brain1.46e-099
collection of basal ganglia1.46e-099
cerebral subcortex1.46e-099
posterior neural tube1.62e-0915
chordal neural plate1.62e-0915
telencephalic nucleus1.84e-097
embryo4.80e-09592
occipital lobe8.75e-095
cell layer1.31e-08309
epithelium1.84e-08306
parietal lobe1.99e-085
embryonic structure5.30e-08564
segmental subdivision of hindbrain6.45e-0812
hindbrain6.45e-0812
presumptive hindbrain6.45e-0812
developing anatomical structure7.96e-08581
germ layer9.60e-08560
germ layer / neural crest9.60e-08560
embryonic tissue9.60e-08560
presumptive structure9.60e-08560
germ layer / neural crest derived structure9.60e-08560
epiblast (generic)9.60e-08560
organ part1.02e-07218
multi-cellular organism2.54e-07656
segmental subdivision of nervous system3.60e-0713
regional part of metencephalon5.63e-079
metencephalon5.63e-079
future metencephalon5.63e-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)
MA0003.11.80249
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.13.07977
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.603517
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.215829
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.12.34702
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.58771
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.14.34317
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.12.01656
MA0146.10.6031
MA0147.10.386018
MA0148.10.653474
MA0149.11.63245
MA0062.21.41923
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.11.91168
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.11.99104
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.146371
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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#1488450.17360027146253.18412825898083e-071.596481859048e-05
CTCF#1066444.288205098460020.005152015588243280.0239387532153107
GABPB1#255345.654147068945740.001776696502096670.0109105901089242
NR3C1#2908411.97841866493849.4122920812787e-050.00136586129314529
YY1#752843.928936599883080.007193866269917620.0298486432546949



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:C1878&oldid=2570389"