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Coexpression cluster:C1743: Difference between revisions

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{{Coexpression_clusters
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056.1;0,MA0057.1;0.189508,MA0058.1;1.29981,MA0059.1;1.29682,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;1.05325,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;0.818263,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;1.15584,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;0.459973,MA0103.1;0.442769,MA0105.1;0.175503,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;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;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;0.938075,MA0145.1;0.143698,MA0146.1;0.946108,MA0147.1;1.77656,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.801354,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;1.54865,MA0047.2;0.767096,MA0112.2;1.96224,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;0.409315,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;1.49262,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.475695,MA0102.2;1.66336,MA0258.1;0.914277,MA0259.1;1.80881,MA0442.1;0}}
|full_id=C1743_cerebellum_pituitary_pineal_lung_parietal_occipital_CD4
|id=C1743
}}

Latest revision as of 11:51, 17 September 2013


Full id: C1743_cerebellum_pituitary_pineal_lung_parietal_occipital_CD4



Phase1 CAGE Peaks

Hg19::chr15:57025759..57025811,-p2@ZNF280D
Hg19::chr15:77197655..77197716,-p1@SCAPER
Hg19::chr18:34409075..34409100,+p1@KIAA1328
Hg19::chr2:113033164..113033219,+p1@ZC3H6
Hg19::chr5:180688105..180688162,-p1@TRIM52


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:0008270zinc ion binding0.00757246536841732
GO:0046914transition metal ion binding0.00757246536841732
GO:0043169cation binding0.0123098686752955
GO:0046872metal ion binding0.0123098686752955
GO:0043167ion binding0.0123098686752955



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
adult organism1.65e-45114
neural tube8.19e-2656
neural rod8.19e-2656
future spinal cord8.19e-2656
neural keel8.19e-2656
nervous system1.25e-2489
regional part of nervous system4.20e-2453
regional part of brain4.20e-2453
central nervous system8.16e-2481
regional part of forebrain8.81e-2241
forebrain8.81e-2241
anterior neural tube8.81e-2241
future forebrain8.81e-2241
brain8.87e-2268
future brain8.87e-2268
brain grey matter1.23e-1734
gray matter1.23e-1734
telencephalon1.49e-1734
regional part of telencephalon1.55e-1632
cerebral hemisphere2.14e-1632
neurectoderm2.23e-1686
neural plate9.42e-1682
presumptive neural plate9.42e-1682
regional part of cerebral cortex4.52e-1322
cerebral cortex1.69e-1225
pallium1.69e-1225
pre-chordal neural plate3.01e-1261
neocortex5.72e-1220
organ system subdivision5.74e-11223
ectoderm-derived structure1.35e-10171
ectoderm1.35e-10171
presumptive ectoderm1.35e-10171
ecto-epithelium7.71e-09104
structure with developmental contribution from neural crest8.08e-08132


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)
MA0003.11.40197
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.12.48957
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
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.10.189508
MA0058.11.29981
MA0059.11.29682
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
MA0073.11.05325
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
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
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.938075
MA0145.10.143698
MA0146.10.946108
MA0147.11.77656
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.21.96224
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.11.49262
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.475695
MA0102.21.66336
MA0258.10.914277
MA0259.11.80881
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
BCLAF1#9774312.99158856607310.0009178032402542550.00667649596774494
CCNT2#90556.336201576962639.78880505817628e-050.00139017271073004
CTCF#1066444.288205098460020.005152015588243280.0239334292331883
E2F4#1874410.13444825222760.0001818201509632970.00220291354367237
E2F6#187644.013724585357910.006632118233933880.0282922880579128
ELF1#199754.258097958807540.0007142416939776840.00572923873097814
GTF2F1#296237.643796526054590.00428415496412050.0203443304823253
HMGN3#932446.542838178680470.00100801277768350.0072205656027769
IRF1#365946.109731002851120.001315525264767990.00880888267789347
MAX#414945.16204440720570.002526309009485180.0139978347202304
MYC#460955.22228187160940.0002573944848850610.00276421826292143
SETDB1#9869216.12801047120420.00585057846659340.0262694997623624
SIN3A#2594244.327107781452110.004977052855762880.0232416017528736
SIX5#147912310.25202921327540.001832291068677690.0108488376280758
SP1#666744.558705102512720.00407573565781680.0194830536601395
SP2#6668210.46141219753790.01353191183347140.0477791453387849
SRF#672238.278306957300690.003404846073776150.0173581333153913
TAF1#687253.343046285745290.002394600090870310.013528596715915
TCF7L2#693448.616141250509880.0003438969725982450.00347318981928132
YY1#752854.911170749853860.00034993140821360.0035266318964026
ZNF143#7702410.80070124178230.0001415223430863190.00184409881342383
ZNF263#1012746.577473309608540.0009875103237900160.00709121223228173



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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