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Coexpression cluster:C2367: Difference between revisions

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{{Coexpression_clusters
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.30702,0.202977,0.170837,0.0604859,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.0201006,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.00178316,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.00825997,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=2.45545,3.43272,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,0.392841,3.55418,1.68405,0.867962,0.341754,0.809319,0.532789,0.559384,2.39977,0.471262,2.52739,0.223552,0.581762,0.169357,1.73475,0.528529,0.632849,0.892087,9.85973,0.728867,1.33003,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,1.59529,3.70541,0.822818,1.65941,0.515703,0.538016,0.90714,1.94963,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,1.8276,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,0.692875,1.32819,0.893276,4.2246,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.17995,2.59699,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,8.3687,2.37404,0.805616,0.632569,4.4082,0.594299,1.14697,0.575476,2.86199,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.95303,0.66252,8.62433,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.91266|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;0.71247,MA0006.1;4.49931,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;1.86845,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;2.82503,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.69331,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.656404,MA0106.1;2.01886,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;2.17614,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;14.2765,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.70272,MA0146.1;0.061409,MA0147.1;3.01834,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;5.8901,MA0047.2;0.856092,MA0112.2;8.86401,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;1.61785,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.57817,MA0163.1;0.918944,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.122011,MA0102.2;1.75932,MA0258.1;4.94877,MA0259.1;3.06353,MA0442.1;0}}
|full_id=C2367_occipital_temporal_brain_postcentral_parietal_paracentral_insula
|id=C2367
}}

Latest revision as of 12:04, 17 September 2013


Full id: C2367_occipital_temporal_brain_postcentral_parietal_paracentral_insula



Phase1 CAGE Peaks

Hg19::chr16:2390672..2390686,-p4@ABCA3
Hg19::chr16:2390692..2390703,-p5@ABCA3
Hg19::chr16:2390704..2390762,-p1@ABCA3
Hg19::chr16:2390769..2390789,-p2@ABCA3


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>

Uber Anatomy
Ontology termp-valuen
adult organism2.01e-34114
neural tube1.29e-2956
neural rod1.29e-2956
future spinal cord1.29e-2956
neural keel1.29e-2956
central nervous system2.83e-2981
nervous system5.59e-2989
regional part of nervous system5.63e-2853
regional part of brain5.63e-2853
neurectoderm4.00e-2586
brain4.47e-2568
future brain4.47e-2568
neural plate6.63e-2582
presumptive neural plate6.63e-2582
anatomical cluster1.44e-23373
regional part of forebrain9.91e-2341
forebrain9.91e-2341
anterior neural tube9.91e-2341
future forebrain9.91e-2341
tube9.61e-22192
telencephalon1.79e-1934
brain grey matter2.58e-1934
gray matter2.58e-1934
pre-chordal neural plate2.65e-1961
cerebral hemisphere2.88e-1832
anatomical conduit3.10e-18240
regional part of telencephalon4.05e-1832
organ system subdivision5.54e-15223
cerebral cortex1.39e-1425
pallium1.39e-1425
regional part of cerebral cortex2.22e-1422
ecto-epithelium3.00e-14104
structure with developmental contribution from neural crest2.01e-13132
neocortex3.23e-1320
ectoderm-derived structure5.64e-11171
ectoderm5.64e-11171
presumptive ectoderm5.64e-11171
epithelium3.03e-10306
cavitated compound organ3.50e-1031
cell layer3.92e-10309
organ part1.01e-09218
kidney1.48e-0926
kidney mesenchyme1.48e-0926
upper urinary tract1.48e-0926
kidney rudiment1.48e-0926
kidney field1.48e-0926
blood vessel endothelium1.14e-0818
endothelium1.14e-0818
cardiovascular system endothelium1.14e-0818
posterior neural tube4.93e-0815
chordal neural plate4.93e-0815
multi-tissue structure6.49e-08342
simple squamous epithelium1.29e-0722
segmental subdivision of nervous system5.07e-0713
squamous epithelium5.19e-0725


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)
MA0003.10.720743
MA0004.10.71247
MA0006.14.49931
MA0007.10.6918
MA0009.11.20602
MA0014.11.86845
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.12.82503
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.12.01886
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.12.17614
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.114.2765
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.10.061409
MA0147.13.01834
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.25.8901
MA0047.20.856092
MA0112.28.86401
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.122011
MA0102.21.75932
MA0258.14.94877
MA0259.13.06353
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
ATF3#467422.46317452600873.92475754624726e-060.000127297438935564
BATF#10538424.35780179230362.83869198020713e-069.77803930477746e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.00014148340712927
BHLHE40#8553444.87181354697742.46312701995675e-071.28302505155742e-05
CCNT2#90546.336201576962630.0006203100587215640.00511726399864309
CEBPB#105147.971147625824820.0002476385788090830.00267872869313742
CHD2#1106410.34402283411698.73193255208051e-050.00129007540501731
CTCF#1066445.360256373075030.001211145381643620.00816649315730378
CTCFL#140690419.74647435897446.5732084880439e-060.000192674521830709
E2F1#186944.907389214879320.001724022357361790.0106421875394827
E2F4#1874412.66806031528443.88145892637771e-050.000726089358430883
E2F6#187645.017155731697390.00157802193473060.00996294479756553
EGR1#195844.988179094810140.001615011500076050.0101376479178052
ELF1#199744.258097958807540.003041525565781240.0160772288978959
ETS1#211349.728760922202340.0001115955317418140.00154410780863583
GABPB1#255347.067683836182170.0004006876864423170.00390076633895872
GTF2F1#2962412.73966087675773.79492332235515e-050.000717224026173453
HEY1#2346244.040111043105710.00375304636917980.0185826771796695
HMGN3#932448.178547723350590.0002234570284440470.00247956104905098
IRF1#365947.63716375356390.0002938853996185490.00307207459220915
IRF4#3662210.95725634337210.01174530180688030.0428350586796374
JUN#3725412.51282919233634.07770316866756e-050.000742453349428994
JUNB#3726430.61063265982111.13787152942193e-064.65484389585967e-05
JUND#372746.994663941871030.000417684217818580.00391303570369166
MAX#414946.452555509007120.0005767613195645490.00485151219829268
MXI1#460149.96157162875930.0001015224754950450.00142263596111995
MYC#460945.22228187160940.001344309395272740.00886913006524885
NFKB1#479045.488063424193840.001102199566301980.00767468634609056
NR3C1#2908414.9730233311731.98868032687801e-050.00044247078112231
NRF1#4899412.21027944771094.49717228915276e-050.000793110734054078
PAX5#507946.669565531177830.0005052774169483260.00443525534952649
RAD21#5885410.35503389545638.6948481184721e-050.00129245835844735
RXRA#6256420.07461713913336.1537798808435e-060.000182066463732412
SETDB1#9869440.32002617801053.77887289069054e-071.85113370464742e-05
SIN3A#2594245.408884726815140.001168172384885160.00795479922442595
SMARCB1#6598418.25271578115749.00423392720929e-060.000241126458236875
SMC3#9126415.04493284493281.95092670935632e-050.000437425578785884
SP1#666745.69838137814090.0009482606065333980.00683662774304443
STAT1#6772420.70658749719925.43610708103893e-060.000165233290872126
TAF1#687243.343046285745290.008005664898701650.0321838267968552
TAF7#6879411.43306940492395.85061525419808e-050.000968202197010289
TBP#690843.706770687096390.005296377814784350.0243903347854078
TCF12#693837.975848676639820.003090920396013070.0162765408782942
TCF7L2#6934410.77017656313737.42969445082454e-050.00115314290199088
USF1#739146.361499277207960.0006105011399140830.00507563513385503
USF2#7392412.99219738506963.50833029870167e-050.000680926422720876
YY1#752844.911170749853860.00171871838055440.0106725268414722
ZBTB7A#5134147.35190930787590.000342223540015990.00346231563457618
ZNF143#7702413.50087655222793.00867915035614e-050.000620259458713077



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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