MCL coexpression mm9:184: Difference between revisions
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|ontology_enrichment_disease= | |ontology_enrichment_disease= | ||
|ontology_enrichment_uberon=UBERON:0002780!5.62e-15!39;UBERON:0001890!5.62e-15!39;UBERON:0006240!5.62e-15!39;UBERON:0000955!1.80e-14!47;UBERON:0006238!1.80e-14!47;UBERON:0003080!1.88e-14!40;UBERON:0002616!2.71e-13!46;UBERON:0003056!5.22e-13!49;UBERON:0003528!2.10e-12!29;UBERON:0002791!2.10e-12!29;UBERON:0001893!2.10e-12!29;UBERON:0000073!1.72e-11!54;UBERON:0001049!4.68e-11!52;UBERON:0005068!4.68e-11!52;UBERON:0006241!4.68e-11!52;UBERON:0007135!4.68e-11!52;UBERON:0002020!6.18e-10!34;UBERON:0000369!7.56e-10!5;UBERON:0002435!7.56e-10!5;UBERON:0000204!7.56e-10!5;UBERON:0010082!7.56e-10!5;UBERON:0002346!1.33e-09!64;UBERON:0003075!1.33e-09!64;UBERON:0007284!1.33e-09!64;UBERON:0001017!7.15e-08!73;UBERON:0002420!7.36e-08!8;UBERON:0007245!7.36e-08!8;UBERON:0010009!7.36e-08!8;UBERON:0010011!7.36e-08!8;UBERON:0000454!7.36e-08!8;UBERON:0010371!1.18e-07!73;UBERON:0001016!1.69e-07!75;UBERON:0001954!7.27e-07!7;UBERON:0003022!7.27e-07!7;UBERON:0002421!7.27e-07!7;UBERON:0000349!7.27e-07!7;UBERON:0002600!7.27e-07!7 | |ontology_enrichment_uberon=UBERON:0002780!5.62e-15!39;UBERON:0001890!5.62e-15!39;UBERON:0006240!5.62e-15!39;UBERON:0000955!1.80e-14!47;UBERON:0006238!1.80e-14!47;UBERON:0003080!1.88e-14!40;UBERON:0002616!2.71e-13!46;UBERON:0003056!5.22e-13!49;UBERON:0003528!2.10e-12!29;UBERON:0002791!2.10e-12!29;UBERON:0001893!2.10e-12!29;UBERON:0000073!1.72e-11!54;UBERON:0001049!4.68e-11!52;UBERON:0005068!4.68e-11!52;UBERON:0006241!4.68e-11!52;UBERON:0007135!4.68e-11!52;UBERON:0002020!6.18e-10!34;UBERON:0000369!7.56e-10!5;UBERON:0002435!7.56e-10!5;UBERON:0000204!7.56e-10!5;UBERON:0010082!7.56e-10!5;UBERON:0002346!1.33e-09!64;UBERON:0003075!1.33e-09!64;UBERON:0007284!1.33e-09!64;UBERON:0001017!7.15e-08!73;UBERON:0002420!7.36e-08!8;UBERON:0007245!7.36e-08!8;UBERON:0010009!7.36e-08!8;UBERON:0010011!7.36e-08!8;UBERON:0000454!7.36e-08!8;UBERON:0010371!1.18e-07!73;UBERON:0001016!1.69e-07!75;UBERON:0001954!7.27e-07!7;UBERON:0003022!7.27e-07!7;UBERON:0002421!7.27e-07!7;UBERON:0000349!7.27e-07!7;UBERON:0002600!7.27e-07!7 | ||
|tfbs_overrepresentation_for_novel_motifs=1.53306,0.221337,1.36862,0.411965,0.725975,0.234508,0.675307,0.0240095,0.0286607,0.883969,1.2753,0.156123,1.31972,0.178347,0.00243098,0,0.399663,0.0904111,0.0434464,0.420889,0.577766,0.0152609,0.177495,0.0399774,0.487408,0.786209,0.860798,0.495219,0.471927,1.11587,0.0990629,0.183906,0.0880249,0.170894,1.41073,0.0802409,2.14109,0.988067,0.0222432,0.263396,0.318713,1.52476,0.0102986,0.0157107,0.788999,0.387046,2.11562,1.66477,0.0940713,0.987107,0.757286,0.0655278,0.251701,0.760373,1.43687,0.413912,0.00456687,0.954455,0.0309639,0.410216,0.512044,0.891917,0.75179,0.112645,0.759959,1.33444,0.393152,0.692274,0.169183,0.561562,0.413173,0.208292,8.46737,0.314307,2.01842,2.83869,0.265123,1.49643,0.161936,0.0337819,0.123394,0.422908,0.241704,0.776317,0.658123,0.854278,1.21325,3.23409,0.305282,1.96251,0.44947,0.665883,0.560088,0.205897,3.45118,0.0930375,0.0541546,0.564259,0.622856,0.0189994,0.276464,0.183736,2.8902,0.118492,1.80341,0.472636,0.456397,0.118042,7.66936,0.847253,0.307043,0.266353,0.597263,0.133363,1.15354,0.313651,0.94288,0.687473,0.401389,0.15237,0.318309,0.102664,0.0566365,2.05187,0.500504,0.953901,1.52328,0.187574,0.39195,0.211845,0.253351,0.0801222,1.71678,0.438966,0.473194,0.94061,0.338633,0.254041,1.10472,1.19378,0.811996,0.396892,0.219399,0.190296,0.74184,0.25263,0.0905195,1.15529,0.34357,0.0417621,1.65252,2.93096,0.278483,0.100862,0.197568,0.338479,0.234185,0.13447,0.157674,0.567238,0.440436,0.656791,0.493371,1.10427,0.113143,0.190296,0.273286,0.0395815,0.51423 | |||
}} | }} |
Revision as of 17:56, 26 November 2012
Phase1 CAGE Peaks
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 ID | GO name | FDR corrected p-value |
---|---|---|
GO:0005667 | transcription factor complex | 2.21598297079184e-06 |
GO:0044451 | nucleoplasm part | 4.71903345537537e-06 |
GO:0005654 | nucleoplasm | 4.71903345537537e-06 |
GO:0044428 | nuclear part | 8.56592444544805e-06 |
GO:0031981 | nuclear lumen | 9.21780987515847e-06 |
GO:0031974 | membrane-enclosed lumen | 1.49106954409539e-05 |
GO:0043233 | organelle lumen | 1.49106954409539e-05 |
GO:0003700 | transcription factor activity | 2.46030139664426e-05 |
GO:0003677 | DNA binding | 3.33490513317119e-05 |
GO:0030182 | neuron differentiation | 3.33490513317119e-05 |
GO:0048699 | generation of neurons | 5.70035228731143e-05 |
GO:0022008 | neurogenesis | 7.37798786953293e-05 |
GO:0043234 | protein complex | 9.60423051146278e-05 |
GO:0001764 | neuron migration | 0.000157786843389063 |
GO:0043565 | sequence-specific DNA binding | 0.000186253501749232 |
GO:0045449 | regulation of transcription | 0.000310268030717556 |
GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.000337541542471085 |
GO:0006350 | transcription | 0.000350968443073521 |
GO:0032991 | macromolecular complex | 0.000368328280140195 |
GO:0010468 | regulation of gene expression | 0.000397195139001037 |
GO:0003676 | nucleic acid binding | 0.000397195139001037 |
GO:0031323 | regulation of cellular metabolic process | 0.000492393669272784 |
GO:0007275 | multicellular organismal development | 0.000539435425325133 |
GO:0003682 | chromatin binding | 0.000539435425325133 |
GO:0019222 | regulation of metabolic process | 0.000565341715550315 |
GO:0007399 | nervous system development | 0.000627396239844129 |
GO:0044446 | intracellular organelle part | 0.000758170481936015 |
GO:0005634 | nucleus | 0.000758170481936015 |
GO:0044422 | organelle part | 0.000758170481936015 |
GO:0048468 | cell development | 0.000773076278392164 |
GO:0048869 | cellular developmental process | 0.000785907451478338 |
GO:0030154 | cell differentiation | 0.000785907451478338 |
GO:0006355 | regulation of transcription, DNA-dependent | 0.00118462929269046 |
GO:0006351 | transcription, DNA-dependent | 0.0012236684118448 |
GO:0032774 | RNA biosynthetic process | 0.0012236684118448 |
GO:0010467 | gene expression | 0.00173410290397194 |
GO:0007420 | brain development | 0.00219247324422909 |
GO:0032502 | developmental process | 0.00243399745371334 |
GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.00321737793986475 |
GO:0048666 | neuron development | 0.00332975180353593 |
GO:0016070 | RNA metabolic process | 0.00356329183884163 |
GO:0007417 | central nervous system development | 0.0037537705428555 |
GO:0021889 | olfactory bulb interneuron differentiation | 0.00428091463779768 |
GO:0050794 | regulation of cellular process | 0.00462055366504015 |
GO:0043283 | biopolymer metabolic process | 0.00462055366504015 |
GO:0016477 | cell migration | 0.00556173952584924 |
GO:0043170 | macromolecule metabolic process | 0.00669180645734662 |
GO:0060163 | subpallium neuron fate commitment | 0.00766724058785636 |
GO:0007411 | axon guidance | 0.00797039814144068 |
GO:0006928 | cell motility | 0.00820820407149906 |
GO:0051674 | localization of cell | 0.00820820407149906 |
GO:0050789 | regulation of biological process | 0.0082387232507014 |
GO:0021988 | olfactory lobe development | 0.00985437040322196 |
GO:0045749 | negative regulation of S phase of mitotic cell cycle | 0.00985437040322196 |
GO:0021772 | olfactory bulb development | 0.00985437040322196 |
GO:0035035 | histone acetyltransferase binding | 0.00985437040322196 |
GO:0030900 | forebrain development | 0.0109073978209299 |
GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.011367274065383 |
GO:0048523 | negative regulation of cellular process | 0.0113689806791655 |
GO:0021798 | forebrain dorsal/ventral pattern formation | 0.0122588499778052 |
GO:0065007 | biological regulation | 0.0131298057511698 |
GO:0048519 | negative regulation of biological process | 0.0131298057511698 |
GO:0006366 | transcription from RNA polymerase II promoter | 0.0131298057511698 |
GO:0021884 | forebrain neuron development | 0.0131298057511698 |
GO:0033261 | regulation of progression through S phase | 0.0131298057511698 |
GO:0045930 | negative regulation of progression through mitotic cell cycle | 0.0131298057511698 |
GO:0021544 | subpallium development | 0.0131298057511698 |
GO:0007090 | regulation of S phase of mitotic cell cycle | 0.0131298057511698 |
GO:0031490 | chromatin DNA binding | 0.0131298057511698 |
GO:0048665 | neuron fate specification | 0.0131298057511698 |
GO:0032501 | multicellular organismal process | 0.0137681597575249 |
GO:0021871 | forebrain regionalization | 0.0151028909639773 |
GO:0007406 | negative regulation of neuroblast proliferation | 0.0151028909639773 |
GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | 0.0162281337282585 |
GO:0051320 | S phase | 0.0164846794619366 |
GO:0001540 | beta-amyloid binding | 0.0164846794619366 |
GO:0021879 | forebrain neuron differentiation | 0.0164846794619366 |
GO:0000084 | S phase of mitotic cell cycle | 0.0164846794619366 |
GO:0043066 | negative regulation of apoptosis | 0.0171580623244607 |
GO:0048731 | system development | 0.0171731729320548 |
GO:0043069 | negative regulation of programmed cell death | 0.0171731729320548 |
GO:0007409 | axonogenesis | 0.0172819807236409 |
GO:0050821 | protein stabilization | 0.0172819807236409 |
GO:0008641 | small protein activating enzyme activity | 0.0172819807236409 |
GO:0021872 | generation of neurons in the forebrain | 0.0172819807236409 |
GO:0048667 | neuron morphogenesis during differentiation | 0.0185426164403585 |
GO:0048812 | neurite morphogenesis | 0.0185426164403585 |
GO:0031647 | regulation of protein stability | 0.0187727410988563 |
GO:0044238 | primary metabolic process | 0.0201624510986748 |
GO:0044237 | cellular metabolic process | 0.0201624510986748 |
GO:0043231 | intracellular membrane-bound organelle | 0.0201624510986748 |
GO:0043227 | membrane-bound organelle | 0.0201624510986748 |
GO:0031519 | PcG protein complex | 0.0216954381239689 |
GO:0000904 | cellular morphogenesis during differentiation | 0.0219034661513601 |
GO:0008134 | transcription factor binding | 0.0219034661513601 |
GO:0045892 | negative regulation of transcription, DNA-dependent | 0.0219034661513601 |
GO:0003727 | single-stranded RNA binding | 0.0226836865020366 |
GO:0031175 | neurite development | 0.0232552390551862 |
GO:0030308 | negative regulation of cell growth | 0.0240689825316621 |
GO:0048856 | anatomical structure development | 0.0263546774688718 |
GO:0030048 | actin filament-based movement | 0.0272025987851738 |
GO:0016481 | negative regulation of transcription | 0.0326944859935074 |
GO:0045792 | negative regulation of cell size | 0.0337395210907081 |
GO:0050768 | negative regulation of neurogenesis | 0.0348264151480951 |
GO:0007346 | regulation of progression through mitotic cell cycle | 0.0348264151480951 |
GO:0045934 | negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0355393243255663 |
GO:0048663 | neuron fate commitment | 0.0355393243255663 |
GO:0021954 | central nervous system neuron development | 0.0355393243255663 |
GO:0032990 | cell part morphogenesis | 0.0368491736529409 |
GO:0048858 | cell projection morphogenesis | 0.0368491736529409 |
GO:0030030 | cell projection organization and biogenesis | 0.0368491736529409 |
GO:0001708 | cell fate specification | 0.0368491736529409 |
GO:0043524 | negative regulation of neuron apoptosis | 0.0368491736529409 |
GO:0021537 | telencephalon development | 0.0368491736529409 |
GO:0021953 | central nervous system neuron differentiation | 0.0381034026033847 |
GO:0045926 | negative regulation of growth | 0.0393348936321501 |
GO:0007405 | neuroblast proliferation | 0.0405442304895145 |
GO:0031324 | negative regulation of cellular metabolic process | 0.0415817369426005 |
GO:0043229 | intracellular organelle | 0.0481335951924562 |
GO:0043226 | organelle | 0.0481335951924562 |
GO:0016874 | ligase activity | 0.0489674259356976 |
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>
Ontology term | p-value | n |
---|---|---|
neuron of cerebral cortex | 9.89e-12 | 6 |
CNS neuron (sensu Vertebrata) | 1.76e-07 | 23 |
neuroblast (sensu Vertebrata) | 1.76e-07 | 23 |
hippocampal neuron | 6.23e-07 | 3 |
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}}} |