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MCL coexpression mm9:1201: Difference between revisions

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{{MCL_coexpression_mm9
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development;0.0288738566240418;13799,104382!GO:0030182;neuron differentiation;0.0288738566240418;13799,104382!GO:0048699;generation of neurons;0.0288738566240418;13799,104382!GO:0022008;neurogenesis;0.0288738566240418;13799,104382!GO:0043565;sequence-specific DNA binding;0.0343317006776549;13799,104382!GO:0030901;midbrain development;0.0343317006776549;13799!GO:0030516;regulation of axon extension;0.0374466075322434;104382!GO:0007399;nervous system development;0.0449113075147967;13799,104382!GO:0048675;axon extension;0.0449113075147967;104382!GO:0001709;cell fate 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|gostat_on_MCL_coexpression=GO:0048666;neuron development;0.0288738566240418;13799,104382!GO:0030182;neuron differentiation;0.0288738566240418;13799,104382!GO:0048699;generation of neurons;0.0288738566240418;13799,104382!GO:0022008;neurogenesis;0.0288738566240418;13799,104382!GO:0043565;sequence-specific DNA binding;0.0343317006776549;13799,104382!GO:0030901;midbrain development;0.0343317006776549;13799!GO:0030516;regulation of axon extension;0.0374466075322434;104382!GO:0007399;nervous system development;0.0449113075147967;13799,104382!GO:0048675;axon extension;0.0449113075147967;104382!GO:0001709;cell fate determination;0.0449113075147967;104382!
|ontology_enrichment_celltype=CL:0000117!3.50e-23!23;CL:0000337!3.50e-23!23;CL:0002319!2.75e-14!43;CL:0000540!4.04e-14!33;CL:0000047!4.04e-14!33;CL:0000031!4.04e-14!33;CL:0000404!4.04e-14!33;CL:0000221!8.66e-14!44;CL:0000133!8.66e-14!44;CL:0000055!1.29e-11!49;CL:0000393!5.73e-11!39;CL:0000211!5.73e-11!39
|ontology_enrichment_disease=
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}}

Latest revision as of 16:33, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr5:106886962..106886973,-p3@Barhl2
Mm9::chr5:106887428..106887437,-p4@Barhl2
Mm9::chr5:106887474..106887489,-p1@Barhl2
Mm9::chr5:106887496..106887515,-p2@Barhl2
Mm9::chr5:28492230..28492257,+p1@En2
Mm9::chr5:28536710..28536719,-p11@Cnpy1
Mm9::chr7:133415927..133415938,+p9@Sbk1


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

GO IDGO nameFDR corrected p-value
GO:0048666neuron development0.0288738566240418
GO:0030182neuron differentiation0.0288738566240418
GO:0048699generation of neurons0.0288738566240418
GO:0022008neurogenesis0.0288738566240418
GO:0043565sequence-specific DNA binding0.0343317006776549
GO:0030901midbrain development0.0343317006776549
GO:0030516regulation of axon extension0.0374466075322434
GO:0007399nervous system development0.0449113075147967
GO:0048675axon extension0.0449113075147967
GO:0001709cell fate determination0.0449113075147967



Relative expression of the co-expression cluster over median <br>Analyst:




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
ectoderm-derived structure3.45e-1595
ectoderm3.45e-1595
presumptive ectoderm3.45e-1595
neurectoderm1.11e-1464
neural plate1.11e-1464
presumptive neural plate1.11e-1464
central nervous system4.28e-1373
nervous system1.75e-1275
ecto-epithelium1.08e-1173
regional part of nervous system3.90e-1154
pre-chordal neural plate1.34e-1049
gray matter7.56e-1034
neural tube1.08e-0952
neural rod1.08e-0952
future spinal cord1.08e-0952
neural keel1.08e-0952
eye4.10e-099
camera-type eye4.10e-099
simple eye4.10e-099
immature eye4.10e-099
ocular region4.10e-099
visual system4.10e-099
face4.10e-099
optic cup4.10e-099
optic vesicle4.10e-099
eye primordium4.10e-099
basal ganglion1.09e-088
nuclear complex of neuraxis1.09e-088
aggregate regional part of brain1.09e-088
collection of basal ganglia1.09e-088
cerebral subcortex1.09e-088
structure with developmental contribution from neural crest1.98e-0792
regional part of spinal cord2.72e-075
gray matter of spinal cord2.72e-075
brain3.50e-0747
future brain3.50e-0747
subdivision of head3.98e-0711


TFBS overrepresentation<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)
MA0003.14.75688
MA0004.12.09829
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.12.85278
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.860672
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.12.33036
MA0046.10.960497
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.756125
MA0058.11.77195
MA0059.10.397033
MA0060.14.42241
MA0061.10.724575
MA0063.10
MA0066.10.616444
MA0067.12.83469
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0210304
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.598004
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.12.39775
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.920496
MA0105.10.488671
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.12.26993
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.304732
MA0146.11.15352
MA0147.12.95213
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.113749
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.21.82979
MA0047.20.626803
MA0112.20.304722
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.15.32313
MA0163.10.519779
MA0164.10.600609
MA0080.20.343316
MA0018.22.52145
MA0099.20.721008
MA0079.23.46801
MA0102.21.65195
MA0258.10.688848
MA0259.12.06728
MA0442.10
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