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{{Coexpression_clusters
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|full_id=C1129_mature_hippocampus_spinal_substantia_corpus_thalamus_breast
|gostat_on_coexpression_clusters=GO:0004621!glycosylphosphatidylinositol phospholipase D activity!0.0127157931504338!2822$GO:0032387!negative regulation of intracellular transport!0.0127157931504338!1410$GO:0004630!phospholipase D activity!0.0254270947850913!2822$GO:0030742!GTP-dependent protein binding!0.0349545369002825!22808
|id=C1129
|ontology_enrichment_celltype=CL:0000055!6.38e-12!180;CL:0000136!1.75e-09!15
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.82e-31!115;UBERON:0001049!4.69e-27!57;UBERON:0005068!4.69e-27!57;UBERON:0006241!4.69e-27!57;UBERON:0007135!4.69e-27!57;UBERON:0005743!4.71e-26!86;UBERON:0001017!1.55e-24!82;UBERON:0002616!3.02e-23!59;UBERON:0003075!3.28e-23!86;UBERON:0007284!3.28e-23!86;UBERON:0000073!3.92e-23!94;UBERON:0001016!3.92e-23!94;UBERON:0000955!1.20e-22!69;UBERON:0006238!1.20e-22!69;UBERON:0003080!1.89e-20!42;UBERON:0002346!4.02e-20!90;UBERON:0000475!7.61e-20!365;UBERON:0002780!8.68e-20!41;UBERON:0001890!8.68e-20!41;UBERON:0006240!8.68e-20!41;UBERON:0002020!8.73e-18!34;UBERON:0003528!8.73e-18!34;UBERON:0001893!1.11e-17!34;UBERON:0000468!1.26e-17!659;UBERON:0000062!2.90e-17!511;UBERON:0002791!4.60e-17!33;UBERON:0004121!6.68e-17!169;UBERON:0000033!1.29e-16!123;UBERON:0001869!1.59e-16!32;UBERON:0000467!2.29e-16!625;UBERON:0000480!4.68e-16!626;UBERON:0003056!1.36e-15!61;UBERON:0000924!3.55e-15!173;UBERON:0006601!3.55e-15!173;UBERON:0000153!6.85e-15!129;UBERON:0007811!6.85e-15!129;UBERON:0000481!6.17e-14!347;UBERON:0002619!5.06e-13!22;UBERON:0000956!1.53e-12!25;UBERON:0000203!1.53e-12!25;UBERON:0001950!8.38e-12!20;UBERON:0002050!1.15e-11!605;UBERON:0005423!1.15e-11!605;UBERON:0000923!1.54e-11!604;UBERON:0005291!1.54e-11!604;UBERON:0006598!1.54e-11!604;UBERON:0002532!1.54e-11!604;UBERON:0000922!1.64e-11!612;UBERON:0000025!3.86e-10!194;UBERON:0000483!1.66e-09!309;UBERON:0004111!2.00e-09!241;UBERON:0000119!3.37e-09!312;UBERON:0000477!3.73e-09!286;UBERON:0000064!1.44e-08!219;UBERON:0003076!9.19e-08!15;UBERON:0003057!9.19e-08!15;UBERON:0002308!8.30e-07!9;UBERON:0000125!8.30e-07!9;UBERON:0002420!8.69e-07!9;UBERON:0007245!8.69e-07!9;UBERON:0010009!8.69e-07!9;UBERON:0010011!8.69e-07!9;UBERON:0000454!8.69e-07!9
}}

Latest revision as of 11:38, 17 September 2013


Full id: C1129_mature_hippocampus_spinal_substantia_corpus_thalamus_breast



Phase1 CAGE Peaks

Hg19::chr11:111782696..111782707,-p3@CRYAB
Hg19::chr3:138067105..138067137,+p6@MRAS
Hg19::chr3:138067461..138067488,+p3@MRAS
Hg19::chr3:138067492..138067519,+p2@MRAS
Hg19::chr3:138067521..138067553,+p5@MRAS
Hg19::chr4:2061045..2061064,+p1@NAT8L
Hg19::chr6:24495348..24495380,-p5@GPLD1


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:0004621glycosylphosphatidylinositol phospholipase D activity0.0127157931504338
GO:0032387negative regulation of intracellular transport0.0127157931504338
GO:0004630phospholipase D activity0.0254270947850913
GO:0030742GTP-dependent protein binding0.0349545369002825



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>

Cell Type
Ontology termp-valuen
fat cell1.57e-0915
Uber Anatomy
Ontology termp-valuen
adult organism1.05e-28114
neural tube5.61e-2656
neural rod5.61e-2656
future spinal cord5.61e-2656
neural keel5.61e-2656
structure with developmental contribution from neural crest1.64e-24132
regional part of nervous system3.91e-2453
regional part of brain3.91e-2453
neural plate4.33e-2282
presumptive neural plate4.33e-2282
central nervous system6.29e-2281
brain5.27e-2168
future brain5.27e-2168
regional part of forebrain3.40e-1941
forebrain3.40e-1941
anterior neural tube3.40e-1941
future forebrain3.40e-1941
nervous system8.45e-1989
multi-cellular organism9.00e-19656
neurectoderm9.30e-1986
anatomical system3.43e-18624
anatomical group7.67e-18625
multi-tissue structure9.89e-18342
organ1.81e-17503
brain grey matter4.11e-1734
gray matter4.11e-1734
telencephalon7.37e-1734
ecto-epithelium3.06e-16104
regional part of telencephalon8.28e-1632
cerebral hemisphere9.53e-1632
pre-chordal neural plate6.66e-1561
developing anatomical structure4.30e-13581
ectoderm-derived structure5.02e-13171
ectoderm5.02e-13171
presumptive ectoderm5.02e-13171
regional part of cerebral cortex1.16e-1222
cerebral cortex6.45e-1225
pallium6.45e-1225
embryonic structure7.38e-12564
embryo8.98e-12592
germ layer9.19e-12560
germ layer / neural crest9.19e-12560
embryonic tissue9.19e-12560
presumptive structure9.19e-12560
germ layer / neural crest derived structure9.19e-12560
epiblast (generic)9.19e-12560
neocortex2.20e-1120
anatomical cluster5.20e-11373
epithelium7.51e-11306
cell layer1.29e-10309
tube4.71e-10192
anatomical conduit1.00e-09240
organ system subdivision2.97e-09223
tissue1.97e-08773
organ part2.51e-08218
posterior neural tube5.85e-0815
chordal neural plate5.85e-0815
neural nucleus8.62e-079
nucleus of brain8.62e-079
basal ganglion9.38e-079
nuclear complex of neuraxis9.38e-079
aggregate regional part of brain9.38e-079
collection of basal ganglia9.38e-079
cerebral subcortex9.38e-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)
MA0003.17.93885
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.14.31657
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.11.8235
MA0050.10.490116
MA0051.10.602745
MA0052.13.42444
MA0055.10.0407081
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.10.198335
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.215865
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.12.24713
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.10.104569
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.04496
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.11.46178
MA0146.10.828373
MA0147.11.40486
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.854285
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.636673
MA0047.20.636643
MA0112.20.556641
MA0065.20.0828768
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.910701
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.17.90932
MA0163.11.30651
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.24.38061
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
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
CTCF#1066453.828754552196450.003387371192681340.0172901451538266
CTCFL#140690411.28369963369960.0002032736265059930.00241328797074677
E2F1#186953.505278010628090.005090553587915050.0236847830965501
E2F6#187653.583682665498130.004598101897827240.0217225839827737
EGR1#195864.275582081265830.0003762130619866450.00373562616284686
HDAC2#306647.666068706643580.0008986373447057820.0066856237101957
RAD21#588557.39645278246880.0001491014505228370.00192294472600081
SMARCB1#6598410.43012330351850.0002755863833009370.00293603654856336
TCF7L2#693446.154386607507050.002064676148138040.0119696204404878
TFAP2A#702037.079414731304980.006452554472180970.028027713214112
TFAP2C#702246.176702062777270.002036754928069020.0118274477582764
ZBTB7A#5134155.251363791339930.0007687692483214460.00603000311869647



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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