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Coexpression cluster:C1574: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;2.72292,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;1.45664,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;2.0635,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;2.41212,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;1.05691,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.791444,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;0.111822,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;1.92154,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;1.16366,MA0103.1;1.12656,MA0105.1;1.00065,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.973423,MA0115.1;1.35895,MA0116.1;3.62647,MA0117.1;1.1512,MA0119.1;0.504689,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;1.39016,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;5.56258,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.0575907,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;5.01961,MA0065.2;1.41695,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;1.91168,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;4.71524,MA0160.1;0.669748,MA0161.1;0,MA0162.1;4.22787,MA0163.1;1.49262,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;1.66926,MA0079.2;13.0494,MA0102.2;1.66336,MA0258.1;0.914277,MA0259.1;2.71109,MA0442.1;0
}}
}}

Revision as of 20:02, 22 January 2013


Full id: C1574_salivary_maxillary_extraskeletal_cerebellum_gastric_breast_alveolar



Phase1 CAGE Peaks

Hg19::chr10:21462980..21462991,-p5@NEBL
Hg19::chr10:21462998..21463062,-p1@NEBL
Hg19::chr10:21463141..21463150,-p6@NEBL
Hg19::chr10:21463243..21463279,-p3@NEBL
Hg19::chr10:21463310..21463319,-p8@NEBL


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
neural tube4.69e-3956
neural rod4.69e-3956
future spinal cord4.69e-3956
neural keel4.69e-3956
regional part of nervous system1.08e-3653
regional part of brain1.08e-3653
adult organism5.99e-34114
neural plate1.57e-2982
presumptive neural plate1.57e-2982
central nervous system4.23e-2981
neurectoderm7.31e-2986
regional part of forebrain1.02e-2841
forebrain1.02e-2841
anterior neural tube1.02e-2841
future forebrain1.02e-2841
brain3.66e-2868
future brain3.66e-2868
nervous system2.43e-2489
brain grey matter1.31e-2334
gray matter1.31e-2334
telencephalon2.12e-2334
ecto-epithelium2.86e-22104
cerebral hemisphere5.22e-2232
regional part of telencephalon7.70e-2232
organ system subdivision5.79e-21223
pre-chordal neural plate5.54e-2061
ectoderm-derived structure7.88e-20171
ectoderm7.88e-20171
presumptive ectoderm7.88e-20171
organ1.30e-18503
structure with developmental contribution from neural crest3.07e-17132
cerebral cortex2.18e-1625
pallium2.18e-1625
regional part of cerebral cortex7.27e-1622
neocortex1.32e-1420
multi-tissue structure2.96e-12342
posterior neural tube2.86e-1115
chordal neural plate2.86e-1115
organ part4.96e-11218
multi-cellular organism7.32e-11656
embryo3.37e-10592
anatomical cluster5.42e-10373
anatomical conduit6.82e-10240
anatomical system7.92e-10624
anatomical group1.04e-09625
segmental subdivision of hindbrain4.48e-0912
hindbrain4.48e-0912
presumptive hindbrain4.48e-0912
neural nucleus8.50e-099
nucleus of brain8.50e-099
developing anatomical structure9.07e-09581
basal ganglion1.11e-089
nuclear complex of neuraxis1.11e-089
aggregate regional part of brain1.11e-089
collection of basal ganglia1.11e-089
cerebral subcortex1.11e-089
tube1.54e-08192
segmental subdivision of nervous system4.80e-0813
germ layer5.06e-08560
germ layer / neural crest5.06e-08560
embryonic tissue5.06e-08560
presumptive structure5.06e-08560
germ layer / neural crest derived structure5.06e-08560
epiblast (generic)5.06e-08560
embryonic structure1.33e-07564
telencephalic nucleus4.96e-077
regional part of metencephalon8.25e-079
metencephalon8.25e-079
future metencephalon8.25e-079
diencephalon9.71e-077
future diencephalon9.71e-077


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)
MA0003.12.72292
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.45664
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
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
MA0048.12.41212
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.111822
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.92154
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.11.16366
MA0103.11.12656
MA0105.11.00065
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.13.62647
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.12.01656
MA0146.15.56258
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.25.01961
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.91168
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.14.71524
MA0160.10.669748
MA0161.10
MA0162.14.22787
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.21.66926
MA0079.213.0494
MA0102.21.66336
MA0258.10.914277
MA0259.12.71109
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-071.59495046158129e-05
CTCF#1066444.288205098460020.005152015588243280.0239185346737438
EGR1#195854.988179094810140.0003237398000590710.00330250644445881
FOS#235358.99795530889441.69470025615156e-050.000388312417841625
FOSL2#2355310.1581203627370.001881990703415430.0110896652603252



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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