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Coexpression cluster:C1994: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.280184,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.161847,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;1.08193,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;5.468,MA0055.1;2.06887,MA0056.1;0,MA0057.1;2.36624,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;2.2047,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;0.0140295,MA0074.1;1.73427,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;1.2972,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;1.36977,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;1.12656,MA0105.1;5.61073,MA0106.1;0.779931,MA0107.1;0.378225,MA0108.2;0.94238,MA0109.1;0,MA0111.1;1.40074,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,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;3.29691,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;3.87914,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;3.4738,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.0118463,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;0.880827,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.81299,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;1.15604,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 20:20, 22 January 2013


Full id: C1994_thyroid_optic_Mast_corpus_substantia_thalamus_anaplastic



Phase1 CAGE Peaks

Hg19::chr7:37488524..37488535,-p15@ELMO1
Hg19::chr7:37488547..37488560,-p6@ELMO1
Hg19::chr7:37488575..37488588,-p9@ELMO1
Hg19::chr7:37488607..37488614,-p21@ELMO1
Hg19::chr7:37488635..37488658,-p16@ELMO1


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
leukocyte2.96e-07136
T cell3.89e-0725
pro-T cell3.89e-0725
mature alpha-beta T cell9.49e-0718
alpha-beta T cell9.49e-0718
immature T cell9.49e-0718
mature T cell9.49e-0718
immature alpha-beta T cell9.49e-0718
Uber Anatomy
Ontology termp-valuen
adult organism3.11e-49114
neural tube1.71e-3456
neural rod1.71e-3456
future spinal cord1.71e-3456
neural keel1.71e-3456
regional part of nervous system8.12e-3253
regional part of brain8.12e-3253
regional part of forebrain4.56e-2741
forebrain4.56e-2741
anterior neural tube4.56e-2741
future forebrain4.56e-2741
central nervous system1.21e-2581
brain3.14e-2568
future brain3.14e-2568
brain grey matter6.84e-2434
gray matter6.84e-2434
telencephalon8.07e-2434
neural plate3.08e-2382
presumptive neural plate3.08e-2382
nervous system4.62e-2289
regional part of telencephalon5.00e-2232
cerebral hemisphere7.64e-2232
neurectoderm3.95e-2186
cerebral cortex1.61e-1625
pallium1.61e-1625
pre-chordal neural plate2.29e-1661
regional part of cerebral cortex3.64e-1522
ecto-epithelium1.40e-14104
neocortex1.48e-1320
structure with developmental contribution from neural crest4.20e-11132
neural nucleus5.85e-099
nucleus of brain5.85e-099
basal ganglion1.45e-089
nuclear complex of neuraxis1.45e-089
aggregate regional part of brain1.45e-089
collection of basal ganglia1.45e-089
cerebral subcortex1.45e-089
posterior neural tube1.46e-0815
chordal neural plate1.46e-0815
organ system subdivision5.70e-08223
brainstem3.20e-076
telencephalic nucleus4.35e-077
segmental subdivision of nervous system5.36e-0713


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)
MA0003.10.280184
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
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
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.15.468
MA0055.12.06887
MA0056.10
MA0057.12.36624
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.12.2047
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0140295
MA0074.11.73427
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.11.12656
MA0105.15.61073
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.13.29691
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.13.87914
MA0140.10.692258
MA0141.10.520334
MA0142.13.4738
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.10.0439995
MA0164.10.810347
MA0080.21.15604
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
CTCF#1066455.360256373075030.0002259278299937090.00250298892932141
E2F6#187655.017155731697390.0003144978599297790.00323285846389824
EBF1#187935.34388010794140.01187615563868110.043247343749938
EGR1#195854.988179094810140.0003237398000590710.00331156326918407
ELF1#199754.258097958807540.0007142416939776840.00573849436705403
GABPB1#255357.067683836182175.6685482528729e-050.000949659144982022
IRF4#3662521.91451268674411.97628413609567e-071.07388729911392e-05
MAX#414956.452555509007128.93743970843928e-050.00130840659617282
MEF2A#4205518.74323090964414.31877656850983e-072.07378715420045e-05
PAX5#507956.669565531177837.57493746384605e-050.00117168082610577
POU2F2#545259.106124057742521.59639992500654e-050.00037017409362291
RAD21#5885510.35503389545638.39503550283973e-060.000230002390577408
REST#597859.650028716128021.19441074361324e-050.000301676091057371
SMC3#9126515.04493284493281.29633924985553e-065.1734189879886e-05
SPI1#668858.204323508522732.68916109982495e-050.000575755014564612
TAF1#687253.343046285745290.002394600090870310.0135564635131399
TBP#690853.706770687096390.001428755106721120.00920415461330171
TCF12#6938510.63446490218647.34844389925727e-060.000211539176514479
TRIM28#10155518.59052504526254.49912775886781e-072.13778163789079e-05
ZNF263#1012758.221841637010682.6606316672286e-050.000572699321297791



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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