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MCL coexpression mm9:399: Difference between revisions

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|gostat_on_MCL_coexpression=GO:0008270;zinc ion binding;0.0109632657125492;21408,232966,22718,237758,22775,22696!GO:0044424;intracellular part;0.0109632657125492;21408,20822,22718,237758,12419,22775,22696,232966,16579,68519!GO:0046914;transition metal ion binding;0.0109632657125492;21408,232966,22718,237758,22775,22696!GO:0046587;positive regulation of calcium-dependent cell-cell adhesion;0.0109632657125492;16579!GO:0016939;kinesin II complex;0.0109632657125492;16579!GO:0046586;regulation of calcium-dependent cell-cell adhesion;0.0109632657125492;16579!GO:0005622;intracellular;0.0109632657125492;21408,20822,22718,237758,12419,22775,22696,232966,16579,68519!GO:0043229;intracellular organelle;0.0170505484654286;21408,22718,237758,12419,22775,22696,232966,16579,68519!GO:0043226;organelle;0.0170505484654286;21408,22718,237758,12419,22775,22696,232966,16579,68519!GO:0005634;nucleus;0.0174100124011624;21408,232966,22718,237758,12419,22775,22696!GO:0043169;cation binding;0.0339239644478828;21408,232966,22718,237758,22775,22696!GO:0010369;chromocenter;0.0344723512049932;12419!GO:0019894;kinesin binding;0.04006297551357;16579!GO:0046872;metal ion binding;0.04006297551357;21408,232966,22718,237758,22775,22696!GO:0022407;regulation of cell-cell adhesion;0.04006297551357;16579!GO:0043167;ion binding;0.04006297551357;21408,232966,22718,237758,22775,22696!GO:0016339;calcium-dependent cell-cell adhesion;0.040515738197994;16579!GO:0045785;positive regulation of cell adhesion;0.0458952073181271;16579!
|gostat_on_MCL_coexpression=GO:0008270;zinc ion binding;0.0109632657125492;21408,232966,22718,237758,22775,22696!GO:0044424;intracellular part;0.0109632657125492;21408,20822,22718,237758,12419,22775,22696,232966,16579,68519!GO:0046914;transition metal ion binding;0.0109632657125492;21408,232966,22718,237758,22775,22696!GO:0046587;positive regulation of calcium-dependent cell-cell adhesion;0.0109632657125492;16579!GO:0016939;kinesin II complex;0.0109632657125492;16579!GO:0046586;regulation of calcium-dependent cell-cell adhesion;0.0109632657125492;16579!GO:0005622;intracellular;0.0109632657125492;21408,20822,22718,237758,12419,22775,22696,232966,16579,68519!GO:0043229;intracellular organelle;0.0170505484654286;21408,22718,237758,12419,22775,22696,232966,16579,68519!GO:0043226;organelle;0.0170505484654286;21408,22718,237758,12419,22775,22696,232966,16579,68519!GO:0005634;nucleus;0.0174100124011624;21408,232966,22718,237758,12419,22775,22696!GO:0043169;cation binding;0.0339239644478828;21408,232966,22718,237758,22775,22696!GO:0010369;chromocenter;0.0344723512049932;12419!GO:0019894;kinesin binding;0.04006297551357;16579!GO:0046872;metal ion binding;0.04006297551357;21408,232966,22718,237758,22775,22696!GO:0022407;regulation of cell-cell adhesion;0.04006297551357;16579!GO:0043167;ion binding;0.04006297551357;21408,232966,22718,237758,22775,22696!GO:0016339;calcium-dependent cell-cell adhesion;0.040515738197994;16579!GO:0045785;positive regulation of cell adhesion;0.0458952073181271;16579!
|ontology_enrichment_celltype=CL:0000540!2.90e-10!33;CL:0000047!2.90e-10!33;CL:0000031!2.90e-10!33;CL:0000404!2.90e-10!33;CL:0000393!1.57e-08!39;CL:0000211!1.57e-08!39;CL:0000117!1.06e-07!23;CL:0000337!1.06e-07!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!2.53e-23!64;UBERON:0003075!2.53e-23!64;UBERON:0007284!2.53e-23!64;UBERON:0010371!6.36e-21!73;UBERON:0004121!9.11e-21!95;UBERON:0000924!9.11e-21!95;UBERON:0006601!9.11e-21!95;UBERON:0001017!2.07e-20!73;UBERON:0003056!4.16e-20!49;UBERON:0001016!4.81e-20!75;UBERON:0010314!1.17e-18!92;UBERON:0000073!1.84e-18!54;UBERON:0001049!4.20e-18!52;UBERON:0005068!4.20e-18!52;UBERON:0006241!4.20e-18!52;UBERON:0007135!4.20e-18!52;UBERON:0000955!2.75e-17!47;UBERON:0006238!2.75e-17!47;UBERON:0002616!1.06e-16!46;UBERON:0003080!4.65e-16!40;UBERON:0002780!1.98e-15!39;UBERON:0001890!1.98e-15!39;UBERON:0006240!1.98e-15!39;UBERON:0002020!6.26e-13!34;UBERON:0003528!3.95e-12!29;UBERON:0002791!3.95e-12!29;UBERON:0001893!3.95e-12!29;UBERON:0000468!5.38e-11!333;UBERON:0000922!4.83e-09!320;UBERON:0000956!8.31e-09!21;UBERON:0001869!8.31e-09!21;UBERON:0000203!8.31e-09!21;UBERON:0002619!4.09e-07!17;UBERON:0000025!6.74e-07!114;UBERON:0002021!9.55e-07!10;UBERON:0000411!9.55e-07!10;UBERON:0001950!9.55e-07!10
}}
}}

Revision as of 20:38, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:50700965..50701027,-p1@Zfp454
Mm9::chr11:50872733..50872809,+p1@Zfp354a
Mm9::chr12:109661279..109661346,+p1@Eml1
Mm9::chr15:103045716..103045792,-p2@Cbx5
Mm9::chr15:12754596..12754638,+p1@Drosha
Mm9::chr16:38550224..38550250,-p2@Poglut1
Mm9::chr17:32967140..32967197,-p1@Zfp799
Mm9::chr1:145624103..145624169,-p1@Trove2
Mm9::chr1:165709942..165709996,+p4@Kifap3
Mm9::chr2:73730355..73730425,-p@chr2:73730355..73730425
-
Mm9::chr4:61869460..61869521,-p1@Zfp37
Mm9::chr7:11080671..11080750,-p1@Zik1
Mm9::chr7:24960051..24960080,+p1@Zfp114
Mm9::chr7:28516417..28516460,+p1@Zfp60
Mm9::chr7:69354369..69354380,-p2@uc009hfe.1
p2@uc012fml.1
Mm9::chr7:69354385..69354432,-p1@uc009hfe.1
p1@uc012fml.1
Mm9::chrX:92853718..92853729,-p3@Zc4h2
Mm9::chrX:92853731..92853751,-p2@Zc4h2
Mm9::chrX:92853755..92853786,-p1@Zc4h2


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:0008270zinc ion binding0.0109632657125492
GO:0044424intracellular part0.0109632657125492
GO:0046914transition metal ion binding0.0109632657125492
GO:0046587positive regulation of calcium-dependent cell-cell adhesion0.0109632657125492
GO:0016939kinesin II complex0.0109632657125492
GO:0046586regulation of calcium-dependent cell-cell adhesion0.0109632657125492
GO:0005622intracellular0.0109632657125492
GO:0043229intracellular organelle0.0170505484654286
GO:0043226organelle0.0170505484654286
GO:0005634nucleus0.0174100124011624
GO:0043169cation binding0.0339239644478828
GO:0010369chromocenter0.0344723512049932
GO:0019894kinesin binding0.04006297551357
GO:0046872metal ion binding0.04006297551357
GO:0022407regulation of cell-cell adhesion0.04006297551357
GO:0043167ion binding0.04006297551357
GO:0016339calcium-dependent cell-cell adhesion0.040515738197994
GO:0045785positive regulation of cell adhesion0.0458952073181271



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>

Cell Type
Ontology termp-valuen
neuron2.90e-1033
neuronal stem cell2.90e-1033
neuroblast2.90e-1033
electrically signaling cell2.90e-1033
electrically responsive cell1.57e-0839
electrically active cell1.57e-0839
CNS neuron (sensu Vertebrata)1.06e-0723
neuroblast (sensu Vertebrata)1.06e-0723

Uber Anatomy
Ontology termp-valuen
neurectoderm2.53e-2364
neural plate2.53e-2364
presumptive neural plate2.53e-2364
ecto-epithelium6.36e-2173
ectoderm-derived structure9.11e-2195
ectoderm9.11e-2195
presumptive ectoderm9.11e-2195
central nervous system2.07e-2073
pre-chordal neural plate4.16e-2049
nervous system4.81e-2075
structure with developmental contribution from neural crest1.17e-1892
regional part of nervous system1.84e-1854
neural tube4.20e-1852
neural rod4.20e-1852
future spinal cord4.20e-1852
neural keel4.20e-1852
brain2.75e-1747
future brain2.75e-1747
regional part of brain1.06e-1646
anterior neural tube4.65e-1640
regional part of forebrain1.98e-1539
forebrain1.98e-1539
future forebrain1.98e-1539
gray matter6.26e-1334
brain grey matter3.95e-1229
regional part of telencephalon3.95e-1229
telencephalon3.95e-1229
multi-cellular organism5.38e-11333
embryo4.83e-09320
cerebral cortex8.31e-0921
cerebral hemisphere8.31e-0921
pallium8.31e-0921
regional part of cerebral cortex4.09e-0717
tube6.74e-07114
occipital lobe9.55e-0710
visual cortex9.55e-0710
neocortex9.55e-0710


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)

{{{tfbs_overrepresentation_jaspar}}}

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