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{{Coexpression_clusters
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|full_id=C3844_MCF7_cervical_occipital_temporal_postcentral_brain_parietal
|id=C3844
|ontology_enrichment_celltype=CL:0000066!1.19e-15!254;CL:0000221!3.34e-09!71;CL:0002076!1.36e-08!43;CL:0000133!2.25e-08!59;CL:0000223!1.09e-07!59;CL:0002319!4.42e-07!25
|ontology_enrichment_disease=DOID:0050687!4.54e-14!143;DOID:305!4.80e-13!106;DOID:162!6.01e-09!235;DOID:14566!2.68e-08!239
|ontology_enrichment_uberon=UBERON:0000924!4.41e-37!173;UBERON:0006601!4.41e-37!173;UBERON:0004121!2.22e-35!169;UBERON:0000073!1.09e-34!94;UBERON:0001016!1.09e-34!94;UBERON:0005743!1.46e-34!86;UBERON:0001017!9.64e-34!82;UBERON:0001049!1.92e-29!57;UBERON:0005068!1.92e-29!57;UBERON:0006241!1.92e-29!57;UBERON:0007135!1.92e-29!57;UBERON:0000955!3.64e-28!69;UBERON:0006238!3.64e-28!69;UBERON:0002346!6.30e-28!90;UBERON:0000033!2.17e-27!123;UBERON:0000153!2.36e-27!129;UBERON:0007811!2.36e-27!129;UBERON:0003075!2.52e-26!86;UBERON:0007284!2.52e-26!86;UBERON:0002616!8.30e-25!59;UBERON:0007023!3.21e-23!115;UBERON:0002780!4.98e-23!41;UBERON:0001890!4.98e-23!41;UBERON:0006240!4.98e-23!41;UBERON:0003080!1.38e-22!42;UBERON:0001893!7.43e-22!34;UBERON:0002020!1.43e-21!34;UBERON:0003528!1.43e-21!34;UBERON:0003056!3.46e-21!61;UBERON:0002791!3.57e-21!33;UBERON:0001869!1.33e-20!32;UBERON:0000956!1.47e-16!25;UBERON:0000203!1.47e-16!25;UBERON:0002619!5.32e-15!22;UBERON:0000064!1.20e-14!219;UBERON:0001950!1.02e-13!20;UBERON:0000062!2.87e-13!511;UBERON:0000475!2.16e-09!365;UBERON:0000922!9.44e-09!612;UBERON:0000481!4.38e-08!347;UBERON:0003076!5.43e-08!15;UBERON:0003057!5.43e-08!15;UBERON:0002050!2.46e-07!605;UBERON:0005423!2.46e-07!605;UBERON:0000923!3.76e-07!604;UBERON:0005291!3.76e-07!604;UBERON:0006598!3.76e-07!604;UBERON:0002532!3.76e-07!604;UBERON:0004732!4.70e-07!13;UBERON:0004119!7.22e-07!169;UBERON:0000925!7.22e-07!169;UBERON:0006595!7.22e-07!169;UBERON:0000477!9.54e-07!286
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3844_MCF7_cervical_occipital_temporal_postcentral_brain_parietal



Phase1 CAGE Peaks

Hg19::chr1:109792151..109792170,+p1@CELSR2
Hg19::chr1:109792197..109792209,+p3@CELSR2
Hg19::chr1:109792214..109792219,+p5@CELSR2


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>disease_data<br>

Cell Type
Ontology termp-valuen
ectodermal cell4.78e-1072
neurectodermal cell1.72e-0959
epithelial cell3.32e-09253
neural cell4.56e-0825
endo-epithelial cell5.44e-0742
Uber Anatomy
Ontology termp-valuen
nervous system7.69e-3789
central nervous system1.71e-3581
ectoderm-derived structure8.06e-35171
ectoderm8.06e-35171
presumptive ectoderm8.06e-35171
neural tube1.21e-3156
neural rod1.21e-3156
future spinal cord1.21e-3156
neural keel1.21e-3156
regional part of nervous system1.40e-2953
regional part of brain1.40e-2953
neurectoderm3.49e-2986
brain1.32e-2868
future brain1.32e-2868
neural plate3.25e-2782
presumptive neural plate3.25e-2782
telencephalon9.15e-2734
ecto-epithelium9.17e-27104
brain grey matter2.53e-2634
gray matter2.53e-2634
adult organism7.26e-26114
regional part of forebrain1.95e-2541
forebrain1.95e-2541
anterior neural tube1.95e-2541
future forebrain1.95e-2541
cerebral hemisphere4.69e-2532
regional part of telencephalon5.73e-2532
organ system subdivision9.07e-23223
pre-chordal neural plate1.32e-2261
cerebral cortex7.00e-2025
pallium7.00e-2025
regional part of cerebral cortex5.85e-1822
neocortex2.82e-1620
structure with developmental contribution from neural crest5.15e-16132
anatomical cluster3.06e-12373
organ part4.96e-11218
organ3.50e-09503
basal ganglion5.79e-089
nuclear complex of neuraxis5.79e-089
aggregate regional part of brain5.79e-089
collection of basal ganglia5.79e-089
cerebral subcortex5.79e-089
neural nucleus7.25e-089
nucleus of brain7.25e-089
embryo8.35e-08592
posterior neural tube1.82e-0715
chordal neural plate1.82e-0715
Disease
Ontology termp-valuen
carcinoma5.38e-14106
cell type cancer3.51e-13143
cancer2.70e-07235


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
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
MA0055.11.67416
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.13.36539
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.21.20011
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
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.13.19905
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
CCNT2#90536.336201576962630.003930750035764890.0190066022957197
E2F1#186934.907389214879320.008460985347239390.0325424191161646
E2F6#187635.017155731697390.00791769806886330.0322246392819459
EGR1#195834.988179094810140.008056488137383440.032068433744195
ETS1#211339.728760922202340.001085840092584840.00762380191122472
GABPB1#255337.067683836182170.002832212825417420.0154139382633544
HMGN3#932438.178547723350590.001827766942164210.0108713566645417
MAX#414936.452555509007120.003721913834265510.0186531483726117
SP1#666735.69838137814090.005403962701712170.0246542224621753
TCF7L2#6934310.77017656313730.0008003181298398380.00613869162473141
YY1#752834.911170749853860.008441455341808260.0329453346204452
ZBTB7A#5134137.35190930787590.002516255860282270.0140209809417926
ZNF263#1012738.221841637010680.001799043925565870.0109423067114422



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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