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{{Coexpression_clusters
{
|full_id=C3589_pineal_Reticulocytes_putamen_amygdala_medial_cerebellum_occipital
 

Latest revision as of 12:29, 17 September 2013


Full id: C3589_pineal_Reticulocytes_putamen_amygdala_medial_cerebellum_occipital



Phase1 CAGE Peaks

Hg19::chr16:75681623..75681648,+p3@TERF2IP
Hg19::chr16:75681650..75681696,+p2@TERF2IP
Hg19::chr16:75681700..75681764,+p1@TERF2IP


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
adult organism6.06e-43114
neural tube3.83e-3156
neural rod3.83e-3156
future spinal cord3.83e-3156
neural keel3.83e-3156
regional part of nervous system1.80e-2953
regional part of brain1.80e-2953
neural plate1.88e-2782
presumptive neural plate1.88e-2782
central nervous system5.62e-2781
nervous system4.78e-2689
neurectoderm9.13e-2686
brain1.38e-2568
future brain1.38e-2568
regional part of forebrain3.17e-2341
forebrain3.17e-2341
anterior neural tube3.17e-2341
future forebrain3.17e-2341
pre-chordal neural plate4.40e-2061
brain grey matter7.80e-1934
gray matter7.80e-1934
telencephalon8.08e-1934
ecto-epithelium1.64e-18104
cerebral hemisphere1.04e-1732
regional part of telencephalon1.25e-1732
structure with developmental contribution from neural crest8.25e-16132
ectoderm-derived structure1.34e-14171
ectoderm1.34e-14171
presumptive ectoderm1.34e-14171
regional part of cerebral cortex5.30e-1422
cerebral cortex1.72e-1325
pallium1.72e-1325
neocortex6.97e-1320
posterior neural tube5.26e-0915
chordal neural plate5.26e-0915
organ system subdivision2.38e-08223
segmental subdivision of nervous system6.53e-0813
segmental subdivision of hindbrain1.88e-0712
hindbrain1.88e-0712
presumptive hindbrain1.88e-0712
basal ganglion6.71e-079
nuclear complex of neuraxis6.71e-079
aggregate regional part of brain6.71e-079
collection of basal ganglia6.71e-079
cerebral subcortex6.71e-079
neural nucleus7.21e-079
nucleus of brain7.21e-079


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.12.94911
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.13.15032
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
MA0071.12.0778
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
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.12.7939
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.22.97249
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
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#90536.336201576962630.003930750035764890.0189758529622469
E2F1#186934.907389214879320.008460985347239390.0324766381961974
EGR1#195834.988179094810140.008056488137383440.0320074393099585
ELF1#199734.258097958807540.01295179875054610.0461505598672222
ETS1#211339.728760922202340.001085840092584840.00761254302406308
FOSL2#2355316.93020060456170.0002060162053171620.0024270870239277
GABPB1#255337.067683836182170.002832212825417420.0153906798102799
GTF2F1#2962312.73966087675770.0004835525047438590.00433454124478104
HMGN3#932438.178547723350590.001827766942164210.0108589880921946
IRF1#365937.63716375356390.002244692747297240.0127889076337885
MAX#414936.452555509007120.003721913834265510.018629011738563
MYC#460935.22228187160940.007020843755740150.0294076321892093
NFKB1#479035.488063424193840.006049381815655430.0269282834986462
NR2C2#7182332.61461090524092.88098172333076e-050.000604554651804183
NRF1#4899312.21027944771090.0005492172401020010.0047070161939121
PAX5#507936.669565531177830.003370290999677260.0172713357073255
POU2F2#545239.106124057742520.001324165192682130.00881193376822537
REST#597839.650028716128020.001112636247114590.0076671032602534
SIN3A#2594235.408884726815140.006318961977991520.0276220521521621
SIX5#147912317.0867153554590.0002004060546325010.00239476063384025
SP1#666735.69838137814090.005403962701712170.0246122916839264
STAT1#6772320.70658749719920.0001125992441046670.00154733584934833
TAF7#6879311.43306940492390.0006690181981945830.00541976354337915
THAP1#55145331.36914460285133.23800758564397e-050.000646234042111734
TRIM28#10155318.59052504526250.0001555969297255280.00196831246894433
YY1#752834.911170749853860.008441455341808260.0328814394466326
ZEB1#6935316.88843201754390.0002075486917327580.00242517093487106



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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