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Coexpression cluster:C486: Difference between revisions

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|ontology_enrichment_disease=DOID:8692!4.36e-19!31;DOID:1240!3.66e-18!39;DOID:2531!1.09e-11!51;DOID:0060083!1.09e-11!51
|ontology_enrichment_disease=DOID:8692!4.36e-19!31;DOID:1240!3.66e-18!39;DOID:2531!1.09e-11!51;DOID:0060083!1.09e-11!51
|ontology_enrichment_uberon=UBERON:0001017!2.99e-35!82;UBERON:0001049!9.14e-35!57;UBERON:0005068!9.14e-35!57;UBERON:0006241!9.14e-35!57;UBERON:0007135!9.14e-35!57;UBERON:0007023!2.37e-34!115;UBERON:0005743!3.09e-33!86;UBERON:0000073!4.75e-31!94;UBERON:0001016!4.75e-31!94;UBERON:0000955!2.92e-30!69;UBERON:0006238!2.92e-30!69;UBERON:0002616!6.19e-29!59;UBERON:0002780!4.89e-27!41;UBERON:0001890!4.89e-27!41;UBERON:0006240!4.89e-27!41;UBERON:0003080!5.26e-26!42;UBERON:0001893!7.98e-26!34;UBERON:0002020!1.17e-25!34;UBERON:0003528!1.17e-25!34;UBERON:0002791!4.09e-25!33;UBERON:0001869!2.59e-24!32;UBERON:0002346!1.81e-22!90;UBERON:0003075!1.41e-20!86;UBERON:0007284!1.41e-20!86;UBERON:0000956!8.76e-19!25;UBERON:0000203!8.76e-19!25;UBERON:0002619!1.54e-16!22;UBERON:0002390!2.98e-15!102;UBERON:0003061!2.98e-15!102;UBERON:0001950!6.39e-15!20;UBERON:0003056!1.72e-14!61;UBERON:0002193!4.90e-13!112;UBERON:0000153!4.09e-12!129;UBERON:0007811!4.09e-12!129;UBERON:0000924!1.47e-11!173;UBERON:0006601!1.47e-11!173;UBERON:0000033!4.51e-11!123;UBERON:0004121!2.52e-10!169;UBERON:0003076!9.01e-10!15;UBERON:0003057!9.01e-10!15;UBERON:0002371!3.06e-09!80;UBERON:0002420!1.00e-08!9;UBERON:0007245!1.00e-08!9;UBERON:0010009!1.00e-08!9;UBERON:0010011!1.00e-08!9;UBERON:0000454!1.00e-08!9;UBERON:0002308!2.55e-08!9;UBERON:0000125!2.55e-08!9;UBERON:0001474!2.92e-08!86;UBERON:0004732!4.17e-08!13;UBERON:0002405!6.35e-08!115;UBERON:0004733!1.26e-07!12;UBERON:0002028!1.26e-07!12;UBERON:0007277!1.26e-07!12;UBERON:0009663!5.48e-07!7
|ontology_enrichment_uberon=UBERON:0001017!2.99e-35!82;UBERON:0001049!9.14e-35!57;UBERON:0005068!9.14e-35!57;UBERON:0006241!9.14e-35!57;UBERON:0007135!9.14e-35!57;UBERON:0007023!2.37e-34!115;UBERON:0005743!3.09e-33!86;UBERON:0000073!4.75e-31!94;UBERON:0001016!4.75e-31!94;UBERON:0000955!2.92e-30!69;UBERON:0006238!2.92e-30!69;UBERON:0002616!6.19e-29!59;UBERON:0002780!4.89e-27!41;UBERON:0001890!4.89e-27!41;UBERON:0006240!4.89e-27!41;UBERON:0003080!5.26e-26!42;UBERON:0001893!7.98e-26!34;UBERON:0002020!1.17e-25!34;UBERON:0003528!1.17e-25!34;UBERON:0002791!4.09e-25!33;UBERON:0001869!2.59e-24!32;UBERON:0002346!1.81e-22!90;UBERON:0003075!1.41e-20!86;UBERON:0007284!1.41e-20!86;UBERON:0000956!8.76e-19!25;UBERON:0000203!8.76e-19!25;UBERON:0002619!1.54e-16!22;UBERON:0002390!2.98e-15!102;UBERON:0003061!2.98e-15!102;UBERON:0001950!6.39e-15!20;UBERON:0003056!1.72e-14!61;UBERON:0002193!4.90e-13!112;UBERON:0000153!4.09e-12!129;UBERON:0007811!4.09e-12!129;UBERON:0000924!1.47e-11!173;UBERON:0006601!1.47e-11!173;UBERON:0000033!4.51e-11!123;UBERON:0004121!2.52e-10!169;UBERON:0003076!9.01e-10!15;UBERON:0003057!9.01e-10!15;UBERON:0002371!3.06e-09!80;UBERON:0002420!1.00e-08!9;UBERON:0007245!1.00e-08!9;UBERON:0010009!1.00e-08!9;UBERON:0010011!1.00e-08!9;UBERON:0000454!1.00e-08!9;UBERON:0002308!2.55e-08!9;UBERON:0000125!2.55e-08!9;UBERON:0001474!2.92e-08!86;UBERON:0004732!4.17e-08!13;UBERON:0002405!6.35e-08!115;UBERON:0004733!1.26e-07!12;UBERON:0002028!1.26e-07!12;UBERON:0007277!1.26e-07!12;UBERON:0009663!5.48e-07!7
|tf_chipseq_enrich=SPI1#6688;7:3.02264550313995:0.00528452342160744:0.0244749597174838
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065,0.555234,0.331013,0.00344453,0.272029,0.343778,0.946628,0.019707,0.510333,0.791952,0.225116,0.322604,0.45078,0.0514516,0.518104,0.169184,0.301502,0.16789,0.879344,0.628028,0.221934,0.0211471,0.301252,0.626648,0.843273,0.203762,0.736826,0.589311,0.825235,0.819853,0.631142,0.090646,0.120323,0.417851,0.721337,0.260597,0.636567,0.619396,0.322604,0.249455,0.445707,0.904276,0.0665147,0.26428,0.468134,0.886957,0.594663,0.399784,0.519206,0.217125,0.5904,0.455286,0.0153247,0.0455334,0.484729,0.277545,0.332498,0.391807,0.463542,0.258829,0.196849,0.386239,0.608674,0.970398,0.00412717,0.204178,0.0231865,0.55245,0.741782,0.129562,0.993443,0.313077,0.265686,0.957638,0.328164,0.705008,0.660841,0.374134,0.476722,0.176543,0.205043,0.0548919,0.704497,0.985245,0.990198,0.768817,0.0732549,0.164821,0.356982,0.517678,0.274506,0.471727,0.0605766,0.0895176,0.256176,0.522686,0.369659,0.802871,0.284534,0.215986,0.227917,0.252957,0.296022,0.536203,0.460925,0.69839,0.504504,0.213277,0.311214,0.81562,0.393769,0.882484,0.649006,0.746735,0.789773,0.492673,0.458416,0.699672,0.491711,0.646968,0.336298,0.153376,0.0837681,0.936267,0.657952,0.376559,0.456944,0.325293,0.627302,0.644413,0.477374,0.655919,0.0322575,0.395396,0.24026,0.487913,0.547313,0.0674219,0.551853,0.425871,0.722827,0.0419083,0.5309,0.72973,0.703774,0.468,0.578069,0.836993,0.616776,0.486089,0.848395,0.499996,0.17688,0.151223,0.324382,0.452228,0.0121406,0.321773,0.0455311,0.415887,0.0105077,0.292214,0.421659,0.664734,0.320079,0.834607,0.353367,0.461799,0.495536,0.422435,0.85973,0.20766,0.0218856,0.0612128,0.24528,0.230583,0.13324,0.334603,0.727077,0.0202012,0.81123,0.732738,0.165254,0.789653,0.0274477,0.726627,0.751759,0.620846,0.540227,0.640389,0.952094,0.011,0.0166994,0.972201,0.297257,0.382837,0.924556,0.814534,0.0356293,0.502966,0.951763,0.945488,0.80437,0.0976634,0.00991666,0.814488,0.356128,0.649279,0.398876,0.914948,0.884768,0.314114,0.903474,0.883543,0.788338,0.916784,0.26312,0.110917,0.00336648,0.176648,0.527078,0.836093,0.607575,0.0854195,0.199038,0.67251,0.271696,0.069932,0.629971,0.794477,0.344302,0.852434,0.777488,0.849851,0.764829,0.716875,0.76316,0.414072,0.0166492,0.394259,0.55986,0.865729,0.75503,0.366491,0.658679,0.25134,0.848851,0.47283,0.42792,0.148471,0.106352,0.00716971,0.555692,0.355209,0.766332,0.4279,0.361726,0.000338076,0.489775,0.854772,0.120109,0.487254,0.914836,0.146062,2.0274e-05,0.936614,0.59934,0.328598,0.991475,0.955389,0.47188,0.00848877,0.0234087,0.55361,0.334095,0.796663,0.765779,0.0163326,0.612059,0.104953,0.685419,0.752437,0.423875,0.69364,0.00372434,0.124854,0.4725,0.0316332,0.504742,0.120693,0.326133,0.0585047,0.820767,0.942625,0.50829,0.763285,0.600109,0.0327414,0.321922,0.0001356,0.869936,0.882931,0.0852088,0.521373,0.0305956,0.673614,0.898995,0.807364,0.0937651,0.938545,0.546068,0.590362,0.0441867,0.458358,0.793088,0.169692,0.750761,0.739835,0.00744972,0.0729057,0.41075,0.546617,0.063229,0.602455,0.00890039,0.404303,0.599835,4.55788e-07,0.333466,0.811728,0.393933,0.772116,0.270321,0.406748,0.247005,0.375202,0.0160083,0.853548,0.392772,0.612095,0.766889,0.12687,0.401692,0.871656,0.766676,0.195233,0.736027,0.850011,0.3806,0.376685,0.579997,0.674902,0.388228,0.676103,0.0745916,0.771679,0.449984,0.133471,0.683547,0.549091,0.355198,0.845682,0.770794,0.517052,0.714158,0.157582,0.468888,0.79766,0.741702,0.681913,0.205706,0.753965,0.376583,0.565509,0.75562,0.189301,0.12866,0.567781,0.71521,0.803994,0.873723,0.432481,0.589402,0.435408,0.537653,0.0232769,0.0730067,0.435679,0.859599,0.532375,0.63114,0.808067,0.673862,0.490028,0.689801,0.00212801,0.351509,0.00506815,0.255671,0.0159318,0.759718,0.514352,0.288581,0.555596,0.14133,0.0375232,0.322215,0.455679,0.664717,0.793236,0.39968,0.205654,0.125957,0.41219,0.716782,0.0259909,0.561653,0.644685,0.0720977,0.567368,0.724809,0.142472,0.082866,0.849552,0.302207,0.0587223,0.782076,0.770848,0.25283,0.742904,0.837064,0.184285,0.80027,0.533937,0.121212,0.757478,0.61466,0.751028,0.0995853,0.095123,0.0129636,0.560844,0.797366,0.336068,0.708323,0.47573,0.418541,0.904991,0.0610231,0.461617,0.41929,0.0154546,0.160994,0.294564,0.295358,0.27811,0.402165,0.231499,0.295178,0.0382459,0.853653,0.443376,0.732022,0.00178617,0.384162,0.415478,0.139993,0.342865,0.561059,0.341641,0.503294,0.352504,0.394885,0.582219,0.00671515,0.248521,0.0101759,0.0225833,0.211091,0.600795,0.0593004,0.891475,0.882305,0.932759,0.074503,0.575861,0.120631,0.413017,0.80499,0.656078,0.0117861,0.710279,0.623643,0.308409,0.591322,0.670178,0.76842,0.755179,0.630922,0.8189,0.710781,0.044531,0.0731045,0.217876,0.539632,0.746817,0.738766,0.619286,0.878628,0.112204,0.315334,0.47773,0.463264,0.91905,0.481656,0.771273,0.471824,0.43392,0.694466,0.696673,0.299342,0.595141,0.373236,0.322893,0.490576,0.215172,0.706399,0.0963263,0.455078,0.842076,0.767893,0.317129
}}
}}

Revision as of 13:25, 5 September 2012


Full id: C486_acute_Neural_chronic_neuroectodermal_caudate_Astrocyte_myelodysplastic



Phase1 CAGE Peaks

Hg19::chr10:105793289..105793301,-p@chr10:105793289..105793301
-
Hg19::chr10:105793325..105793341,-p@chr10:105793325..105793341
-
Hg19::chr10:105793354..105793360,-p@chr10:105793354..105793360
-
Hg19::chr14:23588242..23588262,-p1@CEBPE
Hg19::chr14:23588275..23588288,-p1@CU690200
Hg19::chr14:23588458..23588473,-p2@CEBPE
Hg19::chr16:1537839..1537851,-p@chr16:1537839..1537851
-
Hg19::chr16:1537876..1537921,+p@chr16:1537876..1537921
+
Hg19::chr17:56359033..56359070,-p@chr17:56359033..56359070
-
Hg19::chr22:50523663..50523686,-p7@MLC1
Hg19::chr22:50523689..50523719,-p5@MLC1
Hg19::chr7:2119411..2119445,-p15@MAD1L1
Hg19::chr8:130559296..130559308,+p@chr8:130559296..130559308
+
Hg19::chr8:130695974..130696000,+p@chr8:130695974..130696000
+
Hg19::chr9:100947946..100947962,-p@chr9:100947946..100947962
-
Hg19::chr9:100947965..100947975,-p@chr9:100947965..100947975
-
Hg19::chr9:127148331..127148341,-p@chr9:127148331..127148341
-
Hg19::chr9:127149681..127149698,-p@chr9:127149681..127149698
-
Hg19::chr9:127149714..127149721,-p@chr9:127149714..127149721
-


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:0000093mitotic telophase0.00551925114800423
GO:0051326telophase0.00551925114800423
GO:0000089mitotic metaphase0.00827838931830998
GO:0051323metaphase0.00827838931830998
GO:0051322anaphase0.0091976688152717
GO:0000090mitotic anaphase0.0091976688152717
GO:0000299integral to membrane of membrane fraction0.0126128318365972
GO:0030225macrophage differentiation0.0151734731405287
GO:0007093mitotic cell cycle checkpoint0.0330872449633977
GO:0002573myeloid leukocyte differentiation0.0330872449633977
GO:0006909phagocytosis0.0410950816486348
GO:0000075cell cycle checkpoint0.0477251694968636
GO:0042089cytokine biosynthetic process0.0477251694968636
GO:0007088regulation of mitosis0.0477251694968636
GO:0042107cytokine metabolic process0.0477251694968636
GO:0009059macromolecule biosynthetic process0.0477251694968636
GO:0030099myeloid cell differentiation0.0477251694968636
GO:0005819spindle0.0477251694968636



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
central nervous system2.99e-3582
neural tube9.14e-3557
neural rod9.14e-3557
future spinal cord9.14e-3557
neural keel9.14e-3557
adult organism2.37e-34115
regional part of nervous system4.75e-3194
nervous system4.75e-3194
brain2.92e-3069
future brain2.92e-3069
regional part of brain6.19e-2959
regional part of forebrain4.89e-2741
forebrain4.89e-2741
future forebrain4.89e-2741
anterior neural tube5.26e-2642
telencephalon7.98e-2634
gray matter1.17e-2534
brain grey matter1.17e-2534
regional part of telencephalon4.09e-2533
cerebral hemisphere2.59e-2432
neurectoderm1.81e-2290
neural plate1.41e-2086
presumptive neural plate1.41e-2086
cerebral cortex8.76e-1925
pallium8.76e-1925
regional part of cerebral cortex1.54e-1622
hematopoietic system2.98e-15102
blood island2.98e-15102
neocortex6.39e-1520
pre-chordal neural plate1.72e-1461
hemolymphoid system4.90e-13112
anterior region of body4.09e-12129
craniocervical region4.09e-12129
ectoderm1.47e-11173
presumptive ectoderm1.47e-11173
head4.51e-11123
ectoderm-derived structure2.52e-10169
posterior neural tube9.01e-1015
chordal neural plate9.01e-1015
bone marrow3.06e-0980
basal ganglion1.00e-089
nuclear complex of neuraxis1.00e-089
aggregate regional part of brain1.00e-089
collection of basal ganglia1.00e-089
cerebral subcortex1.00e-089
nucleus of brain2.55e-089
neural nucleus2.55e-089
bone element2.92e-0886
segmental subdivision of nervous system4.17e-0813
immune system6.35e-08115
segmental subdivision of hindbrain1.26e-0712
hindbrain1.26e-0712
presumptive hindbrain1.26e-0712
telencephalic nucleus5.48e-077
Disease
Ontology termp-valuen
myeloid leukemia4.36e-1931
leukemia3.66e-1839
hematologic cancer1.09e-1151
immune system cancer1.09e-1151


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
SPI1#668873.022645503139950.005284523421607440.0244749597174838



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.