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Coexpression cluster:C529: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;14.4455,MA0004.1;0.631966,MA0006.1;2.38286,MA0007.1;0.208008,MA0009.1;0.621697,MA0014.1;20.8865,MA0017.1;0.425352,MA0019.1;0.340029,MA0024.1;0.525161,MA0025.1;0.747404,MA0027.1;2.20546,MA0028.1;0.122394,MA0029.1;0.542771,MA0030.1;0.532314,MA0031.1;0.474026,MA0038.1;0.817744,MA0040.1;0.548121,MA0041.1;0.236024,MA0042.1;0.211928,MA0043.1;0.621991,MA0046.1;0.611559,MA0048.1;2.52644,MA0050.1;0.212584,MA0051.1;0.299199,MA0052.1;0.551663,MA0055.1;0.274153,MA0056.1;0,MA0057.1;0.832754,MA0058.1;0.467197,MA0059.1;0.465036,MA0060.1;0.422819,MA0061.1;1.42092,MA0063.1;0,MA0066.1;0.302992,MA0067.1;0.924196,MA0068.1;0.269471,MA0069.1;0.607975,MA0070.1;0.597583,MA0071.1;0.27142,MA0072.1;0.593415,MA0073.1;7.6252,MA0074.1;0.298586,MA0076.1;0.164578,MA0077.1;0.586275,MA0078.1;0.382364,MA0081.1;0.465308,MA0083.1;0.628701,MA0084.1;1.10674,MA0087.1;0.591148,MA0088.1;2.14055,MA0089.1;0,MA0090.1;0.174619,MA0091.1;1.19125,MA0092.1;0.195947,MA0093.1;0.366841,MA0095.1;0,MA0098.1;0,MA0100.1;1.52405,MA0101.1;0.749201,MA0103.1;0.706501,MA0105.1;0.7537,MA0106.1;0.894258,MA0107.1;0.551112,MA0108.2;0.471286,MA0109.1;0,MA0111.1;0.541878,MA0113.1;0.350573,MA0114.1;1.90309,MA0115.1;0.850405,MA0116.1;1.41998,MA0117.1;1.58019,MA0119.1;0.142224,MA0122.1;0.681203,MA0124.1;0.810546,MA0125.1;0.730403,MA0130.1;0,MA0131.1;1.02939,MA0132.1;0,MA0133.1;0,MA0135.1;0.650071,MA0136.1;0.30842,MA0139.1;0.934169,MA0140.1;0.74193,MA0141.1;0.462123,MA0142.1;0.445733,MA0143.1;0.350722,MA0144.1;0.0651126,MA0145.1;4.34087,MA0146.1;3.60335,MA0147.1;3.24988,MA0148.1;0.240905,MA0149.1;0.261654,MA0062.2;1.38546,MA0035.2;0.268747,MA0039.2;7.99368,MA0138.2;0.997372,MA0002.2;0.0459391,MA0137.2;0.126444,MA0104.2;3.31747,MA0047.2;0.326636,MA0112.2;1.42266,MA0065.2;3.84719,MA0150.1;0.170499,MA0151.1;0,MA0152.1;0.274535,MA0153.1;0.714423,MA0154.1;1.4034,MA0155.1;3.52468,MA0156.1;0.12788,MA0157.1;0.421609,MA0158.1;0,MA0159.1;0.96592,MA0160.1;0.252705,MA0161.1;0,MA0162.1;5.86502,MA0163.1;9.32695,MA0164.1;0.948242,MA0080.2;0.11444,MA0018.2;0.89684,MA0099.2;0.27482,MA0079.2;29.9917,MA0102.2;1.14323,MA0258.1;0.218609,MA0259.1;2.65713,MA0442.1;0
}}
}}

Revision as of 19:14, 22 January 2013


Full id: C529_testis_temporal_amygdala_occipital_insula_brain_putamen



Phase1 CAGE Peaks

Hg19::chr11:125774362..125774414,+p1@DDX25
Hg19::chr12:124457511..124457524,-p6@CCDC92
Hg19::chr12:124457526..124457542,-p7@CCDC92
Hg19::chr12:124457547..124457562,-p8@CCDC92
Hg19::chr12:31882027..31882048,-p3@AMN1
Hg19::chr13:37006421..37006487,+p2@CCNA1
Hg19::chr13:50510622..50510649,-p4@SPRYD7
Hg19::chr14:105940901..105940956,+p2@CRIP2
Hg19::chr15:91446123..91446133,+p14@MAN2A2
Hg19::chr15:91446139..91446156,+p11@MAN2A2
Hg19::chr1:145516574..145516603,+p2@PEX11B
Hg19::chr1:244615425..244615441,-p9@ADSS
Hg19::chr6:43478068..43478103,-p1@LRRC73
Hg19::chr9:90589429..90589488,-p1@CDK20
Hg19::chr9:99212366..99212385,+p2@HABP4
Hg19::chrX:71289516..71289537,+p@chrX:71289516..71289537
+


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:0006167AMP biosynthetic process0.0180732803962082
GO:0033391chromatoid body0.0180732803962082
GO:0046033AMP metabolic process0.0180732803962082
GO:0004572mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity0.0180732803962082
GO:0004019adenylosuccinate synthase activity0.0180732803962082
GO:0007141male meiosis I0.0180732803962082
GO:0005737cytoplasm0.0180732803962082
GO:0007283spermatogenesis0.0180732803962082
GO:0048232male gamete generation0.0180732803962082
GO:0007276gamete generation0.022917850838468
GO:0016559peroxisome fission0.022917850838468
GO:0007140male meiosis0.0245072039266199
GO:0048285organelle fission0.0254315348049321
GO:0019953sexual reproduction0.0254315348049321
GO:0004559alpha-mannosidase activity0.0280008139512107
GO:0006013mannose metabolic process0.0373146430493189
GO:0005779integral to peroxisomal membrane0.0373146430493189
GO:0031231intrinsic to peroxisomal membrane0.0373146430493189
GO:0004004ATP-dependent RNA helicase activity0.0374514524468862
GO:0006406mRNA export from nucleus0.0374514524468862
GO:0008186RNA-dependent ATPase activity0.0374514524468862
GO:0007286spermatid development0.0374514524468862
GO:0015924mannosyl-oligosaccharide mannosidase activity0.0374514524468862
GO:0009167purine ribonucleoside monophosphate metabolic process0.0374514524468862
GO:0048515spermatid differentiation0.0374514524468862
GO:0009168purine ribonucleoside monophosphate biosynthetic process0.0374514524468862
GO:0009127purine nucleoside monophosphate biosynthetic process0.0374514524468862
GO:0009126purine nucleoside monophosphate metabolic process0.0374514524468862
GO:0007031peroxisome organization and biogenesis0.0405746259930195
GO:0006405RNA export from nucleus0.0405746259930195
GO:0003724RNA helicase activity0.0405746259930195
GO:0009161ribonucleoside monophosphate metabolic process0.0419160099579801
GO:0009156ribonucleoside monophosphate biosynthetic process0.0419160099579801
GO:0015923mannosidase activity0.0431412155542507
GO:0009124nucleoside monophosphate biosynthetic process0.0442251507911105
GO:0009123nucleoside monophosphate metabolic process0.0442251507911105
GO:0051168nuclear export0.0479907101573285
GO:0031903microbody membrane0.0479907101573285
GO:0005778peroxisomal membrane0.0479907101573285
GO:0044439peroxisomal part0.0479907101573285
GO:0044438microbody part0.0479907101573285
GO:0000079regulation of cyclin-dependent protein kinase activity0.0488329871421061



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
neural cell1.24e-0825
Uber Anatomy
Ontology termp-valuen
nervous system1.06e-6089
neural tube3.48e-6056
neural rod3.48e-6056
future spinal cord3.48e-6056
neural keel3.48e-6056
central nervous system3.96e-5981
regional part of nervous system5.80e-5753
regional part of brain5.80e-5753
neurectoderm2.34e-5386
brain1.13e-5168
future brain1.13e-5168
neural plate8.19e-5082
presumptive neural plate8.19e-5082
regional part of forebrain3.79e-4441
forebrain3.79e-4441
anterior neural tube3.79e-4441
future forebrain3.79e-4441
pre-chordal neural plate5.70e-4061
adult organism1.17e-39114
ectoderm-derived structure5.45e-38171
ectoderm5.45e-38171
presumptive ectoderm5.45e-38171
ecto-epithelium4.95e-37104
telencephalon1.47e-3634
brain grey matter1.80e-3634
gray matter1.80e-3634
cerebral hemisphere1.60e-3432
regional part of telencephalon3.04e-3432
structure with developmental contribution from neural crest4.13e-31132
cerebral cortex3.20e-2625
pallium3.20e-2625
regional part of cerebral cortex3.42e-2622
organ system subdivision4.61e-24223
neocortex8.77e-2420
posterior neural tube1.60e-1615
chordal neural plate1.60e-1615
anatomical cluster2.29e-15373
segmental subdivision of hindbrain1.44e-1312
hindbrain1.44e-1312
presumptive hindbrain1.44e-1312
segmental subdivision of nervous system3.18e-1213
tube4.72e-12192
basal ganglion5.21e-129
nuclear complex of neuraxis5.21e-129
aggregate regional part of brain5.21e-129
collection of basal ganglia5.21e-129
cerebral subcortex5.21e-129
neural nucleus1.24e-119
nucleus of brain1.24e-119
organ part6.94e-11218
regional part of metencephalon1.91e-109
metencephalon1.91e-109
future metencephalon1.91e-109
embryo1.95e-10592
cell layer7.10e-10309
epithelium7.82e-10306
developing anatomical structure1.47e-09581
telencephalic nucleus1.74e-097
embryonic structure2.69e-09564
germ layer3.63e-09560
germ layer / neural crest3.63e-09560
embryonic tissue3.63e-09560
presumptive structure3.63e-09560
germ layer / neural crest derived structure3.63e-09560
epiblast (generic)3.63e-09560
diencephalon7.23e-097
future diencephalon7.23e-097
gyrus9.58e-096
multi-cellular organism1.12e-08656
multi-tissue structure1.43e-08342
brainstem5.15e-086
limbic system8.19e-085
organ8.45e-08503
anatomical conduit8.79e-08240
temporal lobe1.71e-076
parietal lobe1.78e-075
anatomical system2.32e-07624
occipital lobe2.35e-075
anatomical group2.76e-07625
cerebellum3.42e-076
rhombic lip3.42e-076


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)
MA0003.114.4455
MA0004.10.631966
MA0006.12.38286
MA0007.10.208008
MA0009.10.621697
MA0014.120.8865
MA0017.10.425352
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.817744
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.12.52644
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.274153
MA0056.10
MA0057.10.832754
MA0058.10.467197
MA0059.10.465036
MA0060.10.422819
MA0061.11.42092
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.269471
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.17.6252
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.382364
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.12.14055
MA0089.10
MA0090.10.174619
MA0091.11.19125
MA0092.10.195947
MA0093.10.366841
MA0095.10
MA0098.10
MA0100.11.52405
MA0101.10.749201
MA0103.10.706501
MA0105.10.7537
MA0106.10.894258
MA0107.10.551112
MA0108.20.471286
MA0109.10
MA0111.10.541878
MA0113.10.350573
MA0114.11.90309
MA0115.10.850405
MA0116.11.41998
MA0117.11.58019
MA0119.10.142224
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.11.02939
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.934169
MA0140.10.74193
MA0141.10.462123
MA0142.10.445733
MA0143.10.350722
MA0144.10.0651126
MA0145.14.34087
MA0146.13.60335
MA0147.13.24988
MA0148.10.240905
MA0149.10.261654
MA0062.21.38546
MA0035.20.268747
MA0039.27.99368
MA0138.20.997372
MA0002.20.0459391
MA0137.20.126444
MA0104.23.31747
MA0047.20.326636
MA0112.21.42266
MA0065.23.84719
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.11.4034
MA0155.13.52468
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.96592
MA0160.10.252705
MA0161.10
MA0162.15.86502
MA0163.19.32695
MA0164.10.948242
MA0080.20.11444
MA0018.20.89684
MA0099.20.27482
MA0079.229.9917
MA0102.21.14323
MA0258.10.218609
MA0259.12.65713
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#905103.727177398213316.33214862336528e-050.00103299479861863
CTCFL#14069055.807786576168930.001232243320284070.00828735012731975
E2F1#1869123.464039445797171.12150247414086e-050.000287009548877228
E2F6#187682.361014461975240.01070428057204740.0395172979379306
EGR1#195892.640800697252430.002625082583433610.0145127838616919
ELF1#199792.254287154662810.008076683482994410.0319418640669666
HEY1#2346292.138882316938320.01157345310983340.0422910279324688
HMGN3#9324115.292001468050385.5376987114284e-072.56247991015893e-05
MAX#4149103.795620887651255.38997370122769e-050.000913985165420553
MXI1#460195.273773215225511.18160458251851e-050.000299092586024359
MYC#460982.457544410169130.008361946486306990.0329204361083917
NRF1#489996.46426558996462.18388258131197e-067.84058139943764e-05
PAX5#507972.746291689308520.00825712526082170.0325371983517566
POLR2A#5430141.768490851283120.00279219429261510.0152909642769875
RFX5#599353.543503184469150.01042396886042850.0386848441409387
SIN3A#2594292.86352720831390.001446937093185070.00927722162656733
TAF1#6872101.966497815144290.0124168000695410.0449496770351054
TCF12#693863.753340553712850.003424701508819890.0174516906991774
THAP1#5514547.38097520067090.001759398484930610.0108126290671807
USF2#739253.821234525020470.007612120625264080.0313684606211314
ZNF143#770264.76501525372750.0009979524159249640.00715389885145084
ZNF263#1012762.901826460121420.01212951648882460.0439828682930475



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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