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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 11:43, 17 September 2013


Full id: C1387_Neutrophils_Eosinophils_Whole_brain_parietal_optic_temporal



Phase1 CAGE Peaks

Hg19::chr14:102829269..102829295,+p2@TECPR2
Hg19::chr14:102829302..102829332,+p3@TECPR2
Hg19::chr19:17858547..17858582,+p1@FCHO1
Hg19::chr19:18220958..18221027,+p@chr19:18220958..18221027
+
Hg19::chr19:4969116..4969131,+p1@KDM4B
Hg19::chr3:113557654..113557682,+p3@GRAMD1C


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
adult organism4.33e-33114
neural tube2.20e-2856
neural rod2.20e-2856
future spinal cord2.20e-2856
neural keel2.20e-2856
regional part of nervous system1.83e-2653
regional part of brain1.83e-2653
central nervous system2.23e-2681
nervous system2.53e-2389
brain2.20e-2268
future brain2.20e-2268
neural plate9.84e-2282
presumptive neural plate9.84e-2282
neurectoderm1.36e-2186
regional part of forebrain1.93e-2141
forebrain1.93e-2141
anterior neural tube1.93e-2141
future forebrain1.93e-2141
brain grey matter1.49e-1834
gray matter1.49e-1834
telencephalon1.93e-1834
cerebral hemisphere2.48e-1732
regional part of telencephalon2.57e-1732
pre-chordal neural plate1.36e-1661
hematopoietic system1.69e-1598
blood island1.69e-1598
ecto-epithelium6.92e-15104
hemolymphoid system1.57e-14108
regional part of cerebral cortex1.86e-1422
cerebral cortex2.57e-1325
pallium2.57e-1325
neocortex2.91e-1320
immune system9.88e-1193
bone element5.02e-1082
bone marrow5.91e-1076
structure with developmental contribution from neural crest9.89e-10132
lateral plate mesoderm2.72e-09203
ectoderm-derived structure4.17e-09171
ectoderm4.17e-09171
presumptive ectoderm4.17e-09171
posterior neural tube4.34e-0815
chordal neural plate4.34e-0815
tube1.10e-07192
skeletal element4.10e-0790
segmental subdivision of nervous system6.33e-0713
neural nucleus9.28e-079
nucleus of brain9.28e-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)
MA0003.14.63763
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.85223
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.13.56533
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.71708
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.12.90543
MA0061.10.671725
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.347876
MA0074.10.660398
MA0076.12.07987
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.419295
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.347815
MA0146.12.38407
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.21.22729
MA0035.20.621793
MA0039.26.1078
MA0138.21.80506
MA0002.20.255126
MA0137.20.414885
MA0104.21.35181
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.11.60937
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.12.60605
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.23.96282
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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#90566.336201576962631.54467812014647e-050.000362445828330661
EGR1#195854.156815912341780.001617966818864440.0101324480779147
ELF1#199753.548414965672950.003446837775721690.017528572355193
IRF1#365945.091442502375930.003535240765893810.0179440615449642
IRF3#3661215.66065073716320.006417620989932530.0279142858926144
MEF2A#420539.371615454822030.002687399947103910.0148008945354419
NFKB1#479043.658708949462560.01207927289015230.0438265479025401
PBX3#5090310.95725634337210.001711753441810940.0106883784353278
POLR2A#543062.147453176558070.01019570676818780.0380133306855193
SP1#666743.79892091876060.01052246616798510.0389438266458128
SP2#6668417.43568699589643.01067847232342e-050.000619570933932978
SREBF1#6720323.50292472024410.0001833718571432050.00222042590007874
TFAP2A#702038.259317186522480.003860738477055590.0190436719314792
TFAP2C#702247.206152406573480.0009421413689212550.00681839806172594
ZNF143#770236.750438276113950.006850259204468580.0290390153450296



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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