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{{Coexpression_clusters
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|full_id=C3936_anaplastic_nonsmall_occipital_postcentral_paracentral_frontal_insula
|id=C3936
|ontology_enrichment_celltype=CL:0000333!7.34e-10!41;CL:0000133!1.05e-07!59;CL:0000095!1.19e-07!17;CL:0000123!1.19e-07!17;CL:0000243!9.31e-07!15;CL:0000125!9.31e-07!15;CL:0000030!9.31e-07!15;CL:0000339!9.31e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!4.85e-40!94;UBERON:0001016!4.85e-40!94;UBERON:0000955!1.11e-39!69;UBERON:0006238!1.11e-39!69;UBERON:0001017!1.33e-38!82;UBERON:0001049!1.37e-37!57;UBERON:0005068!1.37e-37!57;UBERON:0006241!1.37e-37!57;UBERON:0007135!1.37e-37!57;UBERON:0005743!1.42e-37!86;UBERON:0002616!9.71e-35!59;UBERON:0003075!3.89e-29!86;UBERON:0007284!3.89e-29!86;UBERON:0003080!2.05e-28!42;UBERON:0002780!3.66e-28!41;UBERON:0001890!3.66e-28!41;UBERON:0006240!3.66e-28!41;UBERON:0002346!1.53e-26!90;UBERON:0001893!1.88e-26!34;UBERON:0002020!5.23e-26!34;UBERON:0003528!5.23e-26!34;UBERON:0002791!1.54e-25!33;UBERON:0001869!4.08e-25!32;UBERON:0000033!7.96e-25!123;UBERON:0004121!3.98e-24!169;UBERON:0000153!3.98e-24!129;UBERON:0007811!3.98e-24!129;UBERON:0007023!4.11e-24!115;UBERON:0003056!2.67e-23!61;UBERON:0000924!1.12e-22!173;UBERON:0006601!1.12e-22!173;UBERON:0000956!6.86e-20!25;UBERON:0000203!6.86e-20!25;UBERON:0002619!7.33e-19!22;UBERON:0001950!2.40e-17!20;UBERON:0000475!2.25e-15!365;UBERON:0000064!1.61e-11!219;UBERON:0003076!3.83e-10!15;UBERON:0003057!3.83e-10!15;UBERON:0004732!1.97e-09!13;UBERON:0004733!1.37e-08!12;UBERON:0002028!1.37e-08!12;UBERON:0007277!1.37e-08!12;UBERON:0002420!1.05e-07!9;UBERON:0007245!1.05e-07!9;UBERON:0010009!1.05e-07!9;UBERON:0010011!1.05e-07!9;UBERON:0000454!1.05e-07!9;UBERON:0002308!1.51e-07!9;UBERON:0000125!1.51e-07!9;UBERON:0000481!2.16e-07!347;UBERON:0001871!3.99e-07!7;UBERON:0000062!4.53e-07!511;UBERON:0002680!5.18e-07!9;UBERON:0001895!5.18e-07!9;UBERON:0010092!5.18e-07!9
}}

Latest revision as of 12:35, 17 September 2013


Full id: C3936_anaplastic_nonsmall_occipital_postcentral_paracentral_frontal_insula



Phase1 CAGE Peaks

Hg19::chr1:211307333..211307357,-p3@KCNH1
Hg19::chr1:211307378..211307389,-p5@KCNH1
Hg19::chr1:211307404..211307472,-p1@KCNH1


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
nervous system2.27e-4389
brain5.17e-4268
future brain5.17e-4268
neural tube1.82e-3956
neural rod1.82e-3956
future spinal cord1.82e-3956
neural keel1.82e-3956
central nervous system8.84e-3981
regional part of nervous system2.09e-3853
regional part of brain2.09e-3853
telencephalon1.19e-2934
brain grey matter2.81e-2934
gray matter2.81e-2934
neural plate7.70e-2982
presumptive neural plate7.70e-2982
regional part of forebrain1.01e-2841
forebrain1.01e-2841
anterior neural tube1.01e-2841
future forebrain1.01e-2841
cerebral hemisphere2.69e-2732
regional part of telencephalon6.62e-2732
neurectoderm9.30e-2786
ecto-epithelium5.60e-23104
pre-chordal neural plate2.74e-2261
cerebral cortex1.53e-2125
pallium1.53e-2125
ectoderm-derived structure4.21e-21171
ectoderm4.21e-21171
presumptive ectoderm4.21e-21171
adult organism1.70e-19114
regional part of cerebral cortex5.60e-1922
neocortex1.01e-1620
structure with developmental contribution from neural crest2.97e-16132
organ system subdivision6.24e-15223
segmental subdivision of nervous system3.40e-1213
posterior neural tube1.15e-1115
chordal neural plate1.15e-1115
segmental subdivision of hindbrain8.67e-1112
hindbrain8.67e-1112
presumptive hindbrain8.67e-1112
gyrus5.66e-106
regional part of metencephalon1.06e-099
metencephalon1.06e-099
future metencephalon1.06e-099
neural nucleus3.79e-099
nucleus of brain3.79e-099
organ part1.30e-08218
parietal lobe2.02e-085
telencephalic nucleus8.00e-077


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)
MA0003.17.68548
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.15.21188
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.13.02012
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.17.54591
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139243450923917
CCNT2#90536.336201576962630.003930750035764890.0190145253814381
CTBP2#1488362.71700033932814.049570681927e-060.000129933367880115
CTCF#1066435.360256373075030.0064925092527670.0279616978907107
CTCFL#140690319.74647435897440.0001298372005551160.00171842192228815
E2F1#186934.907389214879320.008460985347239390.032556806745278
E2F4#1874312.66806031528440.0004917987006298980.00437429437021683
E2F6#187635.017155731697390.00791769806886330.0322447443405737
EGR1#195834.988179094810140.008056488137383440.0320843303939062
ELF1#199734.258097958807540.01295179875054610.0462594613627538
EP300#203336.77394172622320.003216880500103790.0167581695206674
GATA3#2625327.2365163572064.94721007899563e-050.000851766688823318
HMGN3#932438.178547723350590.001827766942164210.0108769317192415
JUND#372736.994663941871030.002921845042734990.0156875680864795
PAX5#507936.669565531177830.003370290999677260.0173018984327219
RAD21#5885310.35503389545630.0009004912073565420.00664404106005721
RXRA#6256320.07461713913330.0001235730348432220.00165311184654686
SMC3#9126315.04493284493280.0002935825420371870.0030927443118642
SPI1#668838.204323508522730.001810593189410520.0109108846638304
TAF7#6879311.43306940492390.0006690181981945830.0054336722607702
USF1#739136.361499277207960.00388404057290560.0190399114477206
YY1#752834.911170749853860.008441455341808260.0329625796172554
ZBTB7A#5134137.35190930787590.002516255860282270.0140307125356124
ZEB1#6935316.88843201754390.0002075486917327580.00242952004212929
ZNF143#7702313.50087655222790.0004062804962997170.00389280080303175
ZNF263#1012738.221841637010680.001799043925565870.010949959120122



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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