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Coexpression cluster:C3469: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!8.42e-78!57;UBERON:0005068!8.42e-78!57;UBERON:0006241!8.42e-78!57;UBERON:0007135!8.42e-78!57;UBERON:0002616!7.92e-68!59;UBERON:0005743!7.69e-66!86;UBERON:0001017!1.99e-64!82;UBERON:0000073!1.10e-60!94;UBERON:0001016!1.10e-60!94;UBERON:0000955!1.20e-57!69;UBERON:0006238!1.20e-57!69;UBERON:0002780!3.75e-54!41;UBERON:0001890!3.75e-54!41;UBERON:0006240!3.75e-54!41;UBERON:0003075!1.10e-53!86;UBERON:0007284!1.10e-53!86;UBERON:0003080!1.26e-52!42;UBERON:0002020!6.59e-52!34;UBERON:0003528!6.59e-52!34;UBERON:0001893!8.37e-52!34;UBERON:0002346!1.28e-50!90;UBERON:0002791!8.08e-50!33;UBERON:0001869!1.04e-48!32;UBERON:0003056!1.77e-37!61;UBERON:0007023!2.56e-37!115;UBERON:0000956!2.02e-35!25;UBERON:0000203!2.02e-35!25;UBERON:0000033!4.73e-32!123;UBERON:0002619!1.55e-30!22;UBERON:0000153!7.03e-30!129;UBERON:0007811!7.03e-30!129;UBERON:0004121!7.20e-28!169;UBERON:0001950!4.25e-27!20;UBERON:0000924!7.50e-27!173;UBERON:0006601!7.50e-27!173;UBERON:0003076!1.66e-25!15;UBERON:0003057!1.66e-25!15;UBERON:0004733!1.05e-23!12;UBERON:0002028!1.05e-23!12;UBERON:0007277!1.05e-23!12;UBERON:0004732!1.25e-21!13;UBERON:0002308!6.32e-18!9;UBERON:0000125!6.32e-18!9;UBERON:0002680!7.44e-18!9;UBERON:0001895!7.44e-18!9;UBERON:0010092!7.44e-18!9;UBERON:0002420!1.42e-17!9;UBERON:0007245!1.42e-17!9;UBERON:0010009!1.42e-17!9;UBERON:0010011!1.42e-17!9;UBERON:0000454!1.42e-17!9;UBERON:0000025!3.38e-16!194;UBERON:0009663!2.83e-14!7;UBERON:0002298!1.12e-12!8;UBERON:0000200!4.07e-12!6;UBERON:0003135!4.13e-12!11;UBERON:0002037!4.68e-12!6;UBERON:0006215!4.68e-12!6;UBERON:0004111!1.18e-11!241;UBERON:0001871!2.55e-11!7;UBERON:0000473!1.57e-10!8;UBERON:0000349!1.94e-10!5;UBERON:0000369!2.28e-09!4;UBERON:0002435!2.28e-09!4;UBERON:0000204!2.28e-09!4;UBERON:0010082!2.28e-09!4;UBERON:0000477!3.12e-09!286;UBERON:0000064!3.22e-09!219;UBERON:0000483!1.07e-07!309;UBERON:0001896!1.59e-07!3;UBERON:0005290!1.59e-07!3;UBERON:0010096!1.59e-07!3;UBERON:0000119!1.71e-07!312;UBERON:0000988!1.73e-07!3;UBERON:0005383!2.29e-07!3;UBERON:0005382!2.29e-07!3;UBERON:0000991!3.50e-07!21;UBERON:0009196!3.50e-07!21;UBERON:0009117!3.50e-07!21;UBERON:0005564!3.50e-07!21;UBERON:0002021!5.91e-07!5;UBERON:0004176!9.11e-07!22;UBERON:0001872!9.93e-07!5
|ontology_enrichment_uberon=UBERON:0001049!8.42e-78!57;UBERON:0005068!8.42e-78!57;UBERON:0006241!8.42e-78!57;UBERON:0007135!8.42e-78!57;UBERON:0002616!7.92e-68!59;UBERON:0005743!7.69e-66!86;UBERON:0001017!1.99e-64!82;UBERON:0000073!1.10e-60!94;UBERON:0001016!1.10e-60!94;UBERON:0000955!1.20e-57!69;UBERON:0006238!1.20e-57!69;UBERON:0002780!3.75e-54!41;UBERON:0001890!3.75e-54!41;UBERON:0006240!3.75e-54!41;UBERON:0003075!1.10e-53!86;UBERON:0007284!1.10e-53!86;UBERON:0003080!1.26e-52!42;UBERON:0002020!6.59e-52!34;UBERON:0003528!6.59e-52!34;UBERON:0001893!8.37e-52!34;UBERON:0002346!1.28e-50!90;UBERON:0002791!8.08e-50!33;UBERON:0001869!1.04e-48!32;UBERON:0003056!1.77e-37!61;UBERON:0007023!2.56e-37!115;UBERON:0000956!2.02e-35!25;UBERON:0000203!2.02e-35!25;UBERON:0000033!4.73e-32!123;UBERON:0002619!1.55e-30!22;UBERON:0000153!7.03e-30!129;UBERON:0007811!7.03e-30!129;UBERON:0004121!7.20e-28!169;UBERON:0001950!4.25e-27!20;UBERON:0000924!7.50e-27!173;UBERON:0006601!7.50e-27!173;UBERON:0003076!1.66e-25!15;UBERON:0003057!1.66e-25!15;UBERON:0004733!1.05e-23!12;UBERON:0002028!1.05e-23!12;UBERON:0007277!1.05e-23!12;UBERON:0004732!1.25e-21!13;UBERON:0002308!6.32e-18!9;UBERON:0000125!6.32e-18!9;UBERON:0002680!7.44e-18!9;UBERON:0001895!7.44e-18!9;UBERON:0010092!7.44e-18!9;UBERON:0002420!1.42e-17!9;UBERON:0007245!1.42e-17!9;UBERON:0010009!1.42e-17!9;UBERON:0010011!1.42e-17!9;UBERON:0000454!1.42e-17!9;UBERON:0000025!3.38e-16!194;UBERON:0009663!2.83e-14!7;UBERON:0002298!1.12e-12!8;UBERON:0000200!4.07e-12!6;UBERON:0003135!4.13e-12!11;UBERON:0002037!4.68e-12!6;UBERON:0006215!4.68e-12!6;UBERON:0004111!1.18e-11!241;UBERON:0001871!2.55e-11!7;UBERON:0000473!1.57e-10!8;UBERON:0000349!1.94e-10!5;UBERON:0000369!2.28e-09!4;UBERON:0002435!2.28e-09!4;UBERON:0000204!2.28e-09!4;UBERON:0010082!2.28e-09!4;UBERON:0000477!3.12e-09!286;UBERON:0000064!3.22e-09!219;UBERON:0000483!1.07e-07!309;UBERON:0001896!1.59e-07!3;UBERON:0005290!1.59e-07!3;UBERON:0010096!1.59e-07!3;UBERON:0000119!1.71e-07!312;UBERON:0000988!1.73e-07!3;UBERON:0005383!2.29e-07!3;UBERON:0005382!2.29e-07!3;UBERON:0000991!3.50e-07!21;UBERON:0009196!3.50e-07!21;UBERON:0009117!3.50e-07!21;UBERON:0005564!3.50e-07!21;UBERON:0002021!5.91e-07!5;UBERON:0004176!9.11e-07!22;UBERON:0001872!9.93e-07!5
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160149,0.123526,0.0906475,0.0558058,0.28262,0.000112257,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0117175,0.0330727,0.00956472,0.02609,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.0376172,0.0286025,0.0470027,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.0353101,0.217069,0.190048,0.131088,0.394069,0.0306378,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.00643528,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00128046,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.0425274,0.739716,0.0926491,0.21727,0.289306,0.119215,0.192475,0.177967,0.0088427,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.0271723,0.291114,0.0355833,0.125606,0.175094,0.000919297,1.28372e-06,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.000415994,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.000479913,0.0282663,0.251466,0.0461822,0.11903,0.0838874,0.00806892,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.0147868,0.0190329,0.00340589,0.184948,0.156261,0.311847,0.0062542,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0161946,0.0743925,0.0360851,0.0998546,0.131093,0.0434602,0.00935312,0.418146,0.36927,0.449036,0.000211816,0.231447,0.00131394,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.00202987,0.000142346,0.580441,0.0863135,0.432035,0.722159,0.390366,0.0049331,0.50058,0.443185,0.00696618,0.3468,0.151996,0.227104,0.518585,0.250246,0.38649,0.284625,0.0344717,0.55194,0.729153,0.0465139,0.164197,0.0252589,0.287881,0.0556235,0.478174,0.336276,0.468444,0.258219,0.119142,0.243383,0.442897,0.00170027,0.73485,0.029557,0.161598,0.405056,0.0868402,0.150692,0.21803,0.0013757,0.454657,0.0282154,0.0201095,0.746954,0.0175763,0.0222555,0.200493,0.20558,0.300504,0.0361545,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,4.6719e-05,0.0101316,0.000835245,0.230581,0.120226,0.0448825,0.0513026,0.314429,0.181415,0.00475227,0.446891,0.0727621,0.408413,0.516511,0.322213,0.28903,0.33942,0.0156581,0.387276,0.522605,4.99296e-05,0.180745,0.222037,0.416621,0.416292,0.462712,0.382478,0.215157,0.0225745,0.452428,0.138871,0.00583733,0.166905,0.19783,0.0833851,0.056391,0.48065,0.175199,0.332919,0.373557,0.0393909,0.0164118,0.0111982,0.534741,0.39088,0.363192,0.236011,0.203486,0.0413386,0.375787,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.035296,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.127092,0.283463,0.00164832,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.138622,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.0664606,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.00455899,0.0855609,0.131118,0.20837,0.247588,6.79935e-06,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,9.99207e-07,0.201602,0.350452,0.154941,1.01156e-05,0.0986735,0.00610703,0.0595618,0.0251995,0.158479,0.220319,0.195218,0.124213,0.0370716,0.30793,0.0173907,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.00193951,0.207559,0.141867,0.0199603,0.249101,0.115972,0.224568,0.246105,0.0159159,0.200432,0.139785,0.197112,1.85911e-08,0.156465,1.45157e-05,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,6.31569e-08,0.218161,0.0822373,0.202065,0.00591081,0.0536053,0.0537737,0.0120432,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.00908908,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.0440463,0.283218,0.0342254,0.00084829,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.00259055,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.0228361,0.361435
}}
}}

Revision as of 13:13, 5 September 2012


Full id: C3469_pons_iPS_non_H9_diencephalon_teratocarcinoma_HES3GFP



Phase1 CAGE Peaks

Hg19::chr14:96343250..96343261,+p3@ENST00000554321
Hg19::chr14:96343264..96343291,+p2@ENST00000554321
Hg19::chr14:96343299..96343304,+p4@ENST00000554321


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>

Cell Type
Ontology termp-valuen
embryonic stem cell3.32e-125
oligodendrocyte8.16e-107
macroglial cell8.16e-107
astrocyte8.16e-107
oligodendrocyte precursor cell8.16e-107
Uber Anatomy
Ontology termp-valuen
neural tube8.42e-7857
neural rod8.42e-7857
future spinal cord8.42e-7857
neural keel8.42e-7857
regional part of brain7.92e-6859
central nervous system1.99e-6482
regional part of nervous system1.10e-6094
nervous system1.10e-6094
brain1.20e-5769
future brain1.20e-5769
regional part of forebrain3.75e-5441
forebrain3.75e-5441
future forebrain3.75e-5441
neural plate1.10e-5386
presumptive neural plate1.10e-5386
anterior neural tube1.26e-5242
gray matter6.59e-5234
brain grey matter6.59e-5234
telencephalon8.37e-5234
neurectoderm1.28e-5090
regional part of telencephalon8.08e-5033
cerebral hemisphere1.04e-4832
pre-chordal neural plate1.77e-3761
adult organism2.56e-37115
cerebral cortex2.02e-3525
pallium2.02e-3525
head4.73e-32123
regional part of cerebral cortex1.55e-3022
anterior region of body7.03e-30129
craniocervical region7.03e-30129
ectoderm-derived structure7.20e-28169
neocortex4.25e-2720
ectoderm7.50e-27173
presumptive ectoderm7.50e-27173
posterior neural tube1.66e-2515
chordal neural plate1.66e-2515
segmental subdivision of hindbrain1.05e-2312
hindbrain1.05e-2312
presumptive hindbrain1.05e-2312
segmental subdivision of nervous system1.25e-2113
nucleus of brain6.32e-189
neural nucleus6.32e-189
regional part of metencephalon7.44e-189
metencephalon7.44e-189
future metencephalon7.44e-189
basal ganglion1.42e-179
nuclear complex of neuraxis1.42e-179
aggregate regional part of brain1.42e-179
collection of basal ganglia1.42e-179
cerebral subcortex1.42e-179
tube3.38e-16194
telencephalic nucleus2.83e-147
brainstem1.12e-128
gyrus4.07e-126
male reproductive organ4.13e-1211
cerebellum4.68e-126
rhombic lip4.68e-126
anatomical conduit1.18e-11241
temporal lobe2.55e-117
testis1.57e-108
limbic system1.94e-105
corpus striatum2.28e-094
striatum2.28e-094
ventral part of telencephalon2.28e-094
future corpus striatum2.28e-094
anatomical cluster3.12e-09286
organ part3.22e-09219
epithelium1.07e-07309
medulla oblongata1.59e-073
myelencephalon1.59e-073
future myelencephalon1.59e-073
cell layer1.71e-07312
pons1.73e-073
caudate-putamen2.29e-073
dorsal striatum2.29e-073
gonad3.50e-0721
indifferent external genitalia3.50e-0721
indifferent gonad3.50e-0721
gonad primordium3.50e-0721
occipital lobe5.91e-075
external genitalia9.11e-0722
parietal lobe9.93e-075


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
CTCF#1066435.360256373075030.0064925092527670.0278938324838428
RAD21#5885310.35503389545630.0009004912073565420.00662998951040605



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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