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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.205340976140048,-

Latest revision as of 12:46, 17 September 2013


Full id: C4459_Eosinophils_Neutrophils_CD14_occipital_postcentral_parietal_medial



Phase1 CAGE Peaks

Hg19::chr5:130599701..130599716,+p2@CDC42SE2
Hg19::chr7:97736163..97736190,+p1@LMTK2
Hg19::chr7:97736234..97736245,+p2@LMTK2


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:0004864protein phosphatase inhibitor activity0.0243568701007585
GO:0019212phosphatase inhibitor activity0.0243568701007585
GO:0016301kinase activity0.0243568701007585
GO:0046777protein amino acid autophosphorylation0.0243568701007585
GO:0016540protein autoprocessing0.0243568701007585
GO:0016772transferase activity, transferring phosphorus-containing groups0.0249784497864923
GO:0019888protein phosphatase regulator activity0.0271223419769981
GO:0019208phosphatase regulator activity0.0271223419769981
GO:0016485protein processing0.0290996119542236
GO:0016740transferase activity0.0416052735611413



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
adult organism1.41e-33114
neural tube2.33e-2156
neural rod2.33e-2156
future spinal cord2.33e-2156
neural keel2.33e-2156
regional part of nervous system7.22e-2153
regional part of brain7.22e-2153
regional part of forebrain1.83e-1941
forebrain1.83e-1941
anterior neural tube1.83e-1941
future forebrain1.83e-1941
central nervous system1.37e-1781
brain grey matter7.24e-1734
gray matter7.24e-1734
telencephalon7.57e-1734
nervous system9.18e-1789
cerebral hemisphere1.90e-1632
brain4.10e-1668
future brain4.10e-1668
regional part of telencephalon6.42e-1632
regional part of cerebral cortex5.43e-1522
neocortex7.28e-1420
cerebral cortex8.26e-1325
pallium8.26e-1325
neurectoderm2.20e-1286
neural plate3.13e-1282
presumptive neural plate3.13e-1282
organ system subdivision3.04e-11223
pre-chordal neural plate8.61e-1161
ecto-epithelium8.80e-08104
hematopoietic system4.58e-0798
blood island4.58e-0798


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0055.11.06172
MA0056.10
MA0057.10.886807
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
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
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
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.11.70974
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.12.94916
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.14.34338
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.22.28794
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
ATF3#467214.97544968400580.005768294540793880.0259681414520441
BRCA1#672213.45615376214920.007119807716084560.0296414573092623
CCNT2#90536.336201576962630.003930750035764890.0190808088768417
CHD2#1106310.34402283411690.0009033701102746880.00662363598335988
CTCFL#140690213.16431623931620.007433367036996010.030692394242778
E2F1#186934.907389214879320.008460985347239390.032703806390834
E2F6#187635.017155731697390.00791769806886330.0323785766323667
EGR1#195834.988179094810140.008056488137383440.0321985138749498
ELF1#199734.258097958807540.01295179875054610.0464309514882876
ETS1#211339.728760922202340.001085840092584840.00764332772322354
HMGN3#932438.178547723350590.001827766942164210.0109030244272726
IRF1#365937.63716375356390.002244692747297240.0128583515705889
JUND#372736.994663941871030.002921845042734990.0157409767057773
NFKB1#479035.488063424193840.006049381815655430.027050496122848
NFYA#4800212.28372046655370.008516011403724430.0324896334244228
NFYB#4801211.17319550235760.01025467135054530.0381500951511986
NR3C1#290829.982015554115360.01278474365547170.0460692765632892
PAX5#507936.669565531177830.003370290999677260.0173479458706404
PBX3#5090214.60967512449610.006056122473217890.0268564126780351
POU2F2#545239.106124057742520.001324165192682130.008848015902657
SIN3A#2594235.408884726815140.006318961977991520.0277883729849449
SMC3#9126210.02995522995520.0126656379767470.0457790816630379
SP2#6668217.43568699589640.004273568481769740.0203273315419934
YY1#752834.911170749853860.008441455341808260.0330763545600327
ZEB1#6935211.25895467836260.01010222676646330.03782413641868



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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