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Coexpression cluster:C986: Difference between revisions

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{{Coexpression_clusters
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acid binding!0.0204835785567552!55814;546;1060;23318;54856$GO:0003677!DNA binding!0.0228631337756485!55814;546;1060;54856$GO:0005720!nuclear heterochromatin!0.0330563092809218!546$GO:0044427!chromosomal part!0.0330563092809218!546;1060$GO:0005694!chromosome!0.0330563092809218!546;1060$GO:0000792!heterochromatin!0.0330563092809218!546$GO:0000790!nuclear chromatin!0.0330563092809218!546$GO:0006306!DNA methylation!0.0330563092809218!546$GO:0006305!DNA alkylation!0.0330563092809218!546$GO:0006304!DNA modification!0.0333998818179596!546$GO:0005634!nucleus!0.0333998818179596!55814;546;1060;54856$GO:0000776!kinetochore!0.0333998818179596!1060$GO:0043414!biopolymer methylation!0.0447173103598427!546$GO:0003678!DNA helicase 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0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.131075,MA0074.1;0.552456,MA0076.1;1.74818,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.770971,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.818737,MA0095.1;0,MA0098.1;0,MA0100.1;1.40058,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.586268,MA0106.1;0.59853,MA0107.1;0.666147,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.470675,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.220937,MA0146.1;0.113833,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;1.50503,MA0035.2;0.515566,MA0039.2;0.164269,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.0572179,MA0065.2;1.27835,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.0799828,MA0155.1;0.0535085,MA0156.1;0.865715,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.378102,MA0163.1;0.0517199,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;1.46097,MA0099.2;0.523145,MA0079.2;3.09265,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0}}
|full_id=C986_cerebellum_CD4_granulocyte_Mast_pineal_non_pituitary
|id=C986
}}

Latest revision as of 11:35, 17 September 2013


Full id: C986_cerebellum_CD4_granulocyte_Mast_pineal_non_pituitary



Phase1 CAGE Peaks

Hg19::chr11:107328527..107328569,-p1@CWF19L2
Hg19::chr13:107220455..107220517,-p1@ARGLU1
Hg19::chr1:155826967..155827018,-p1@GON4L
Hg19::chr1:53018743..53018777,-p1@ZCCHC11
Hg19::chr4:68411245..68411267,-p3@CENPC1
Hg19::chr5:70751463..70751503,+p1@BDP1
Hg19::chr6:99873145..99873196,-p1@PNISR
Hg19::chrX:77041685..77041716,-p1@ATRX


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:0003676nucleic acid binding0.0204835785567552
GO:0003677DNA binding0.0228631337756485
GO:0005720nuclear heterochromatin0.0330563092809218
GO:0044427chromosomal part0.0330563092809218
GO:0005694chromosome0.0330563092809218
GO:0000792heterochromatin0.0330563092809218
GO:0000790nuclear chromatin0.0330563092809218
GO:0006306DNA methylation0.0330563092809218
GO:0006305DNA alkylation0.0330563092809218
GO:0006304DNA modification0.0333998818179596
GO:0005634nucleus0.0333998818179596
GO:0000776kinetochore0.0333998818179596
GO:0043414biopolymer methylation0.0447173103598427
GO:0003678DNA helicase activity0.0452035226043505



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 organism5.32e-25114
neural tube7.34e-1756
neural rod7.34e-1756
future spinal cord7.34e-1756
neural keel7.34e-1756
regional part of nervous system1.27e-1553
regional part of brain1.27e-1553
nervous system1.43e-1589
regional part of forebrain5.55e-1541
forebrain5.55e-1541
anterior neural tube5.55e-1541
future forebrain5.55e-1541
central nervous system1.03e-1481
brain6.76e-1368
future brain6.76e-1368
brain grey matter3.14e-1234
gray matter3.14e-1234
telencephalon1.32e-1134
regional part of telencephalon2.00e-1132
cerebral hemisphere4.56e-1132
neurectoderm2.56e-1086
neural plate9.58e-1082
presumptive neural plate9.58e-1082
regional part of cerebral cortex1.09e-0822
cerebral cortex2.03e-0825
pallium2.03e-0825
neocortex8.34e-0820
pre-chordal neural plate9.27e-0861


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)
MA0003.10.00718652
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.11.52958
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.835832
MA0056.10
MA0057.11.56323
MA0058.10.950944
MA0059.10.361075
MA0060.11.06021
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.131075
MA0074.10.552456
MA0076.11.74818
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.11.40058
MA0101.10.30624
MA0103.10.291333
MA0105.10.586268
MA0106.10.59853
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.220937
MA0146.10.113833
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.21.50503
MA0035.20.515566
MA0039.20.164269
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.21.27835
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.0535085
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.378102
MA0163.10.0517199
MA0164.10.627336
MA0080.20.303167
MA0018.21.46097
MA0099.20.523145
MA0079.23.09265
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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#46738.423690447253280.004171166389609930.0198719298679168
E2F1#186963.680541911159490.001366491550819140.00899388776632215
ELF1#199784.258097958807549.24826870984006e-060.000246712627276369
FOXA1#316956.925887343365910.0002650891078941710.00283838849080986
FOXA2#317039.236423907249470.003211939548395410.016844175470493
GABPB1#255354.417302397613860.002182228654850360.0125882230590399
HEY1#2346284.040111043105711.4081650274634e-050.000339490644744346
IRF1#365954.773227345977440.001525548480294670.0097150462032619
MXI1#460144.980785814379650.005094415320429170.0236974720136425
MYC#460953.263926169755880.008583639497943430.0327046341076836
NFKB1#479064.116047568145380.0007299856589784310.00581754843479957
POLR2A#543082.147453176558070.002210725788971910.0127308111311445
POU2F2#545255.691327536089080.000670954773528490.00541612657230963
RFX5#599346.023955413597550.00252649680619860.0139921942911536
SIN3A#2594264.056663545111350.000792208907523070.00612870415502236
SIX5#14791248.54335767772950.000677999305962630.00547003240752654
SP1#666753.561488361338060.005813761866596070.0261356523581882
SRF#672246.89858913108390.001522071904568780.00970118806549854
TAF1#687283.343046285745296.40776711117462e-050.00104451504498824
TAF7#687968.574802053692941.07203127640034e-050.000278097055330291
TBP#690883.706770687096392.80450451364125e-050.000592674315864383
THAP1#55145311.76342922606920.001607377924306930.0101231950212079
YY1#752884.911170749853862.95299276601526e-060.000101117249668809



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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