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Coexpression cluster:C1537: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!1.25e-27!86;UBERON:0001049!4.71e-27!57;UBERON:0005068!4.71e-27!57;UBERON:0006241!4.71e-27!57;UBERON:0007135!4.71e-27!57;UBERON:0001017!6.40e-27!82;UBERON:0000073!3.16e-25!94;UBERON:0001016!3.16e-25!94;UBERON:0000467!1.69e-24!625;UBERON:0000468!2.29e-24!659;UBERON:0000480!3.29e-24!626;UBERON:0002616!6.14e-23!59;UBERON:0000955!8.53e-23!69;UBERON:0006238!8.53e-23!69;UBERON:0000033!3.07e-22!123;UBERON:0000922!3.85e-22!612;UBERON:0003075!1.24e-21!86;UBERON:0007284!1.24e-21!86;UBERON:0002050!1.30e-21!605;UBERON:0005423!1.30e-21!605;UBERON:0004121!3.52e-21!169;UBERON:0000923!3.63e-21!604;UBERON:0005291!3.63e-21!604;UBERON:0006598!3.63e-21!604;UBERON:0002532!3.63e-21!604;UBERON:0000062!7.52e-21!511;UBERON:0000153!9.36e-21!129;UBERON:0007811!9.36e-21!129;UBERON:0007023!1.37e-20!115;UBERON:0000924!1.51e-20!173;UBERON:0006601!1.51e-20!173;UBERON:0002346!1.83e-20!90;UBERON:0000477!1.96e-20!286;UBERON:0004111!5.03e-20!241;UBERON:0003080!1.17e-19!42;UBERON:0002780!2.03e-19!41;UBERON:0001890!2.03e-19!41;UBERON:0006240!2.03e-19!41;UBERON:0002020!1.89e-17!34;UBERON:0003528!1.89e-17!34;UBERON:0001893!3.82e-17!34;UBERON:0002791!9.27e-17!33;UBERON:0000025!4.16e-16!194;UBERON:0001869!5.53e-16!32;UBERON:0003056!2.19e-15!61;UBERON:0000481!6.35e-15!347;UBERON:0000475!6.44e-15!365;UBERON:0000956!1.67e-12!25;UBERON:0000203!1.67e-12!25;UBERON:0000064!3.86e-11!219;UBERON:0000483!5.73e-11!309;UBERON:0002619!1.24e-10!22;UBERON:0000119!2.39e-10!312;UBERON:0001950!1.52e-09!20;UBERON:0003076!1.47e-08!15;UBERON:0003057!1.47e-08!15;UBERON:0004732!4.96e-07!13;UBERON:0004733!9.14e-07!12;UBERON:0002028!9.14e-07!12;UBERON:0007277!9.14e-07!12
|ontology_enrichment_uberon=UBERON:0005743!1.25e-27!86;UBERON:0001049!4.71e-27!57;UBERON:0005068!4.71e-27!57;UBERON:0006241!4.71e-27!57;UBERON:0007135!4.71e-27!57;UBERON:0001017!6.40e-27!82;UBERON:0000073!3.16e-25!94;UBERON:0001016!3.16e-25!94;UBERON:0000467!1.69e-24!625;UBERON:0000468!2.29e-24!659;UBERON:0000480!3.29e-24!626;UBERON:0002616!6.14e-23!59;UBERON:0000955!8.53e-23!69;UBERON:0006238!8.53e-23!69;UBERON:0000033!3.07e-22!123;UBERON:0000922!3.85e-22!612;UBERON:0003075!1.24e-21!86;UBERON:0007284!1.24e-21!86;UBERON:0002050!1.30e-21!605;UBERON:0005423!1.30e-21!605;UBERON:0004121!3.52e-21!169;UBERON:0000923!3.63e-21!604;UBERON:0005291!3.63e-21!604;UBERON:0006598!3.63e-21!604;UBERON:0002532!3.63e-21!604;UBERON:0000062!7.52e-21!511;UBERON:0000153!9.36e-21!129;UBERON:0007811!9.36e-21!129;UBERON:0007023!1.37e-20!115;UBERON:0000924!1.51e-20!173;UBERON:0006601!1.51e-20!173;UBERON:0002346!1.83e-20!90;UBERON:0000477!1.96e-20!286;UBERON:0004111!5.03e-20!241;UBERON:0003080!1.17e-19!42;UBERON:0002780!2.03e-19!41;UBERON:0001890!2.03e-19!41;UBERON:0006240!2.03e-19!41;UBERON:0002020!1.89e-17!34;UBERON:0003528!1.89e-17!34;UBERON:0001893!3.82e-17!34;UBERON:0002791!9.27e-17!33;UBERON:0000025!4.16e-16!194;UBERON:0001869!5.53e-16!32;UBERON:0003056!2.19e-15!61;UBERON:0000481!6.35e-15!347;UBERON:0000475!6.44e-15!365;UBERON:0000956!1.67e-12!25;UBERON:0000203!1.67e-12!25;UBERON:0000064!3.86e-11!219;UBERON:0000483!5.73e-11!309;UBERON:0002619!1.24e-10!22;UBERON:0000119!2.39e-10!312;UBERON:0001950!1.52e-09!20;UBERON:0003076!1.47e-08!15;UBERON:0003057!1.47e-08!15;UBERON:0004732!4.96e-07!13;UBERON:0004733!9.14e-07!12;UBERON:0002028!9.14e-07!12;UBERON:0007277!9.14e-07!12
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0289867,0.127078,0.378656,0.392439,0.153874,0.145835,0.0494127,0.0696034,0.106792,0.149864,0.109211,0.081783,0.0678906,0.076236,0.444489,0.31161,0.0751154,0.0953991,0.319245,0.236827,0.0650516,0.0560806,0.390908,0.0773818,0.115736,0.662745,0.229952,0.205891,0.207936,0.454529,0.0563868,0.023361,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.0806655,0.417985,0.491614,0.146453,0.315229,0.157053,0.062493,0.00153888,0.273582,0.262915,0.306556,0.26147,0.170005,0.523331,0.491788,0.092369,0.18076,0.11609,0.248113,0.000618943,0.206465,0.240599,0.245625,0.410665,0.00751986,0.100989,0.00130877,0.0975693,0.00748558,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.0560882,0.0651555,0.387334,0.494914,0.224219,0.347904,0.0594064,0.795569,0.111827,0.0929171,0.63152,0.118035,0.319902,0.510835,0.000483593,0.397628,0.0327122,0.0699003,0.235435,0.00714451,0.0042899,0.191316,0.370285,0.388777,0.204831,0.130161,4.45418e-06,0.0963721,0.182511,0.369139,0.145449,0.0892237,0.208284,0.135613,0.401189,0.283386,0.0739625,5.78113e-07,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.491435,0.00471061,0.0708038,0.0879364,0.192889,0.00135257,0.316041,0.565635,0.0435468,0.121421,0.00931917,0.275075,0.167651,0.287361,0.138613,0.00103442,0.116846,0.267784,0.278571,0.185281,0.0454821,0.31159,0.349805,0.255609,0.000202238,0.439697,0.493192,0.00224681,0.160738,0.00145231,0.213489,0.212611,0.338443,0.319005,0.180695,0.45842,0.436073,0.261316,0.189596,0.120497,0.196587,0.213353,0.0504588,0.307626,0.173101,0.259063,0.306056,0.341713,0.156156,0.33569,0.0461852,0.526446,0.761719,0.114697,0.0200942,0.324956,0.000160409,0.408751,0.648685,0.576023,0.070868,0.654476,0.245,0.0850317,0.249379,0.661446,0.0664865,0.696439,0.648789,0.409327,0.466607,0.685907,0.603176,0.670776,0.696176,0.355968,0.636386,0.592254,0.647186,0.616927,0.0088307,0.0586453,0.677416,0.000334755,0.628346,0.0471089,0.750579,0.326884,0.772379,0.0106895,0.00112497,0.0948545,0.000799452,0.573004,0.623606,0.145412,0.754734,0.799242,0.735002,0.494578,0.00589327,0.711296,0.492887,0.819065,0.0431797,0.559471,0.0395776,0.0228595,0.6937,0.0002836,0.0337266,0.629087,0.275995,0.403716,0.297082,0.0236856,0.342233,0.746016,0.00180476,0.0152821,0.0374358,0.72684,0.000347724,0.0606986,0.031375,0.36546,0.0011715,0.368898,0.510705,0.119581,0.670481,0.00192063,0.619669,0.287839,0.262665,0.654187,0.00118451,0.0411767,0.218878,0.300816,0.407994,0.225997,0.487688,0.230404,0.529993,0.00794549,0.484887,7.51676e-07,0.852842,0.650025,0.179563,0.0442901,0.00164492,0.563634,0.561918,0.0177676,0.772094,0.834029,0.201655,0.394773,0.659669,0.659285,0.0375679,0.929537,0.823122,0.0778516,0.121495,0.258457,0.000115996,0.305952,0.0102991,0.159817,0.0419695,0.730276,0.0576354,0.555004,0.607569,0.773067,0.650555,0.231104,0.198803,0.261107,0.594475,0.416321,0.000111484,0.47205,0.0156647,0.116922,0.0571946,0.474879,0.0176389,0.518205,0.424119,0.60488,0.519279,0.515179,0.159275,0.076169,0.414645,0.438945,0.619652,0.706112,0.167767,0.39196,0.000683581,0.355152,0.346355,0.354044,0.115549,0.520214,0.127385,0.486574,5.94788e-05,0.722202,0.639482,0.471879,0.600697,0.136393,0.621275,0.727464,0.589415,0.564042,0.0728165,0.0419954,9.47172e-07,0.55481,0.443148,0.160346,0.145092,0.0115271,0.321667,0.149733,0.477082,0.078203,0.066291,0.343349,0.0230279,0.341084,0.138667,0.459605,0.298707,1.7791e-08,0.299527,0.390707,0.0013619,0.172033,0.181635,0.304651,0.440771,0.613566,0.118662,0.371991,0.694395,0.326635,0.349721,0.39301,0.396235,0.566617,0.039723,0.0877354,0.357781,0.338712,0.231439,0.359148,0.0641227,0.0168593,0.232711,0.00774694,0.402268,0.479755,0.163801,0.245045,0.080461,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.40549,0.30902,0.00292531,0.12783,0.101672,0.0890286,0.00389839,0.362561,0.213995,0.285875,0.225945,0.18761,0.20516,0.115576,0.385234,0.0474652,0.392097,0.352327,0.232997,0.451856,0.521039,0.328594,0.294205,0.0226154,0.278746,0.00162276,0.232479,0.334662,2.70024e-07,0.139427,0.450171,0.454978,5.44626e-07,0.0845395,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.316114,0.00117004,0.26003,0.0101875,0.0184757,0.288449,0.00300003,0.447896,0.395958,0.314638,0.322324,0.184473,0.363414,0.0396204,0.0294149,0.00165513,0.157712,0.000107502,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.043357,0.454949,0.378002,0.340219,0.0169449,0.00906252,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.156256,0.491191,0.0552601,0.263371,0.0241922,0.446399,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.00364611,1.18737e-05,0.295506,0.0788916,0.358783,0.491474,0.417013,0.544575,0.21822,0.388558,0.0149063,0.21727,0.351946,0.345508,0.0296607,0.00484044,1.78629e-07,0.0511051,0.398223,0.178399,0.547908,0.400541,0.0800337,0.182559,1.34448e-06,0.533328,0.313891,0.292462,0.46896,0.137165,0.467981,0.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}}
}}

Revision as of 13:53, 5 September 2012


Full id: C1537_clear_endometrial_serous_Neural_Fibroblast_CD14_melanoma



Phase1 CAGE Peaks

Hg19::chr7:20370300..20370359,+p1@ITGB8
Hg19::chr7:20370483..20370513,+p3@ITGB8
Hg19::chr7:20370516..20370553,+p2@ITGB8
Hg19::chr7:20370652..20370663,+p12@ITGB8
Hg19::chr7:20370666..20370680,+p5@ITGB8
Hg19::chr7:20370694..20370705,+p15@ITGB8


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 tube4.71e-2757
neural rod4.71e-2757
future spinal cord4.71e-2757
neural keel4.71e-2757
central nervous system6.40e-2782
regional part of nervous system3.16e-2594
nervous system3.16e-2594
anatomical system1.69e-24625
multi-cellular organism2.29e-24659
anatomical group3.29e-24626
regional part of brain6.14e-2359
brain8.53e-2369
future brain8.53e-2369
head3.07e-22123
embryo3.85e-22612
neural plate1.24e-2186
presumptive neural plate1.24e-2186
embryonic structure1.30e-21605
developing anatomical structure1.30e-21605
ectoderm-derived structure3.52e-21169
germ layer3.63e-21604
embryonic tissue3.63e-21604
presumptive structure3.63e-21604
epiblast (generic)3.63e-21604
organ7.52e-21511
anterior region of body9.36e-21129
craniocervical region9.36e-21129
adult organism1.37e-20115
ectoderm1.51e-20173
presumptive ectoderm1.51e-20173
neurectoderm1.83e-2090
anatomical cluster1.96e-20286
anatomical conduit5.03e-20241
anterior neural tube1.17e-1942
regional part of forebrain2.03e-1941
forebrain2.03e-1941
future forebrain2.03e-1941
gray matter1.89e-1734
brain grey matter1.89e-1734
telencephalon3.82e-1734
regional part of telencephalon9.27e-1733
tube4.16e-16194
cerebral hemisphere5.53e-1632
pre-chordal neural plate2.19e-1561
multi-tissue structure6.35e-15347
organism subdivision6.44e-15365
cerebral cortex1.67e-1225
pallium1.67e-1225
organ part3.86e-11219
epithelium5.73e-11309
regional part of cerebral cortex1.24e-1022
cell layer2.39e-10312
neocortex1.52e-0920
posterior neural tube1.47e-0815
chordal neural plate1.47e-0815
segmental subdivision of nervous system4.96e-0713
segmental subdivision of hindbrain9.14e-0712
hindbrain9.14e-0712
presumptive hindbrain9.14e-0712


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)

{{{tfbs_overrepresentation_jaspar}}}



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
BATF#10538312.17890089615180.00125981487125340.00846297069137669
CTCF#1066465.360256373075034.21437267579784e-050.000756392623969154
E2F1#186964.907389214879327.15746523583771e-050.00112815954084765
E2F6#187665.017155731697396.26776799983417e-050.00102537503467212
EBF1#187957.422055705474179.7002838805275e-050.00138022881225942
EGR1#195854.156815912341780.001617966818864440.0101360948110721
ESR1#2099630.76860329615451.17571957705476e-091.07711383252651e-07
FOXA1#3169611.08141974938555.39600313513231e-072.51025911550148e-05
IRF4#3662621.91451268674419.01304984425575e-096.9011283921131e-07
JUND#372744.663109294580680.004917643408260230.0229929605549219
MAX#414966.452555509007121.3848964723355e-050.000334808339523721
MXI1#460169.96157162875931.02262624227062e-064.30653476276214e-05
MYC#460965.22228187160944.92821127172503e-050.000854837164935544
NR3C1#2908614.9730233311738.86442195171695e-085.25122725022897e-06
PAX5#507966.669565531177831.13557256338955e-050.000290112678443838
POLR2A#543062.147453176558070.01019570676818780.0380758570822701
RAD21#5885610.35503389545638.10515055094479e-073.54775280129976e-05
SMARCB1#6598412.16847718743830.0001234985463193470.0016608375842192
SMARCC1#6599643.66335931963151.43811211260506e-101.52482224292751e-08
SP1#666765.69838137814092.91961319085282e-050.000610086998878508
TAF1#687263.343046285745290.0007162474284635620.00573871616273924
TBP#690863.706770687096390.000385416472907960.00378170903927419
TFAP2C#7022610.80922860986026.2644941908553e-072.86829245418122e-05
TRIM28#10155412.39368336350830.0001149534924635960.00157285835181521



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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