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Coexpression cluster:C2081: Difference between revisions

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{{Coexpression_clusters
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,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.111581,0.184359,0.334474,0.00761927,0.257476,0.291176,0.376537,0.0588457,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.000147325,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,1.92131,0.395818,0.392841,0.151681,1.68405,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.223552,0.581762,0.169357,1.73475,1.3102,1.53003,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,1.59701,0.183156,0.53106,1.59529,0.61613,1.92371,0.694903,0.173425,2.28614,2.09659,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,0.393426,1.02706,0.844545,5.28917,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.823598,1.00941,1.08,0.62601,0.362435,2.33882,0.844168,0.399165,1.27559,0.353274,0.221873,0.291738,0.934646,1.89266,1.51507,2.78853,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,2.50078,1.14983,1.05974,0.979006,2.81371,1.04326,0.805616,1.52945,2.21427,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,2.16698,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,5.61573,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,2.75236,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.156682|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,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;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.69331,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.01899,MA0061.1;1.68681,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.841508,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;3.33774,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;6.20284,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;1.62583,MA0089.1;0,MA0090.1;0.640115,MA0091.1;4.13319,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;3.24733,MA0101.1;1.33363,MA0103.1;0.521546,MA0105.1;1.90157,MA0106.1;0.869173,MA0107.1;2.98058,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;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;1.08195,MA0146.1;0.221129,MA0147.1;3.01834,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.777367,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;2.6968,MA0047.2;0.856092,MA0112.2;0.187982,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;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.20937,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;3.06353,MA0442.1;0}}
|full_id=C2081_corpus_medulla_substantia_pons_optic_thalamus_globus
|id=C2081
}}

Latest revision as of 11:58, 17 September 2013


Full id: C2081_corpus_medulla_substantia_pons_optic_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr10:96162180..96162235,+p3@TBC1D12
Hg19::chr10:96162242..96162283,+p2@TBC1D12
Hg19::chr10:96162285..96162309,+p1@TBC1D12
Hg19::chr10:96162321..96162343,+p4@TBC1D12


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 organism1.00e-23114
organ2.22e-23503
neural tube1.61e-2156
neural rod1.61e-2156
future spinal cord1.61e-2156
neural keel1.61e-2156
brain6.67e-2068
future brain6.67e-2068
regional part of nervous system1.15e-1953
regional part of brain1.15e-1953
central nervous system2.47e-1981
nervous system4.00e-1889
neural plate2.36e-1682
presumptive neural plate2.36e-1682
regional part of forebrain3.00e-1641
forebrain3.00e-1641
anterior neural tube3.00e-1641
future forebrain3.00e-1641
multi-cellular organism7.19e-16656
anatomical group9.46e-16625
anatomical system1.43e-15624
brain grey matter7.22e-1534
gray matter7.22e-1534
telencephalon7.26e-1534
neurectoderm6.09e-1486
regional part of telencephalon1.29e-1332
cerebral hemisphere1.44e-1332
bone marrow7.24e-1376
bone element8.01e-1382
pre-chordal neural plate1.78e-1161
skeletal system2.02e-11100
ecto-epithelium2.06e-11104
developing anatomical structure4.23e-11581
skeletal element8.75e-1190
germ layer9.22e-11560
germ layer / neural crest9.22e-11560
embryonic tissue9.22e-11560
presumptive structure9.22e-11560
germ layer / neural crest derived structure9.22e-11560
epiblast (generic)9.22e-11560
organ system subdivision1.12e-10223
embryonic structure1.60e-10564
immune system2.21e-1093
regional part of cerebral cortex3.59e-1022
cerebral cortex9.22e-1025
pallium9.22e-1025
structure with developmental contribution from neural crest1.26e-09132
embryo1.98e-09592
neocortex4.61e-0920
hematopoietic system4.94e-0998
blood island4.94e-0998
hemolymphoid system3.30e-08108
ectoderm-derived structure6.49e-08171
ectoderm6.49e-08171
presumptive ectoderm6.49e-08171
neural nucleus6.98e-079
nucleus of brain6.98e-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)
MA0003.10.0214529
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.13.33774
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.16.20284
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.14.13319
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.13.24733
MA0101.11.33363
MA0103.10.521546
MA0105.11.90157
MA0106.10.869173
MA0107.12.98058
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
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.10.221129
MA0147.13.01834
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.22.6968
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.10.418966
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
CCNT2#90546.336201576962630.0006203100587215640.00511120806491688
E2F1#186944.907389214879320.001724022357361790.0106227239516524
E2F4#1874412.66806031528443.88145892637771e-050.000725439672176023
E2F6#187645.017155731697390.00157802193473060.00994791047512096
EBF1#187948.9064668465690.00015887907472010.00199341322497508
EGR1#195844.988179094810140.001615011500076050.0101248686029439
GABPB1#255347.067683836182170.0004006876864423170.00389677076863294
GATA3#2625427.2365163572061.81561517799785e-066.74088281460779e-05
HEY1#2346244.040111043105710.00375304636917980.0185457492193409
MAFK#7975427.10073313782991.85228494563408e-066.84055118235778e-05
MAX#414946.452555509007120.0005767613195645490.0048437098306531
MYC#460945.22228187160940.001344309395272740.00885514531270195
NFKB1#479045.488063424193840.001102199566301980.0076639560922112
NRF1#4899412.21027944771094.49717228915276e-050.000791640277611369
PAX5#507946.669565531177830.0005052774169483260.00443004265855156
PBX3#5090421.91451268674414.33289161192893e-060.000135933573763366
SP1#666745.69838137814090.0009482606065333980.0068295558572334
SP2#6668426.15353049384462.13562021071447e-067.73645644074953e-05
STAT1#6772420.70658749719925.43610708103893e-060.000164945260731152
TAF1#687243.343046285745290.008005664898701650.0321133675048203
TBP#690843.706770687096390.005296377814784350.0243420349673589
TCF12#6938410.63446490218647.8163066689251e-050.00119854243458504
USF1#739146.361499277207960.0006105011399140830.00506958166108666
YY1#752844.911170749853860.00171871838055440.0106592178709454
ZBTB7A#5134147.35190930787590.000342223540015990.00345863018151054
ZNF143#7702413.50087655222793.00867915035614e-050.000619403591137482
ZNF263#1012736.166381227758010.006539814347975980.0279567627476675



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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