Personal tools

MCL coexpression mm9:1876: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 7: Line 7:
|ontology_enrichment_uberon=UBERON:0000468!5.76e-08!333
|ontology_enrichment_uberon=UBERON:0000468!5.76e-08!333
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,0.612053,0.688265,0.483253,0.704257,1.88411,0.370124,1.76086,0.162942,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,1.50428,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.854272,0.503207,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,3.2365,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,1.4408,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,1.75347,0.580757,0.57247,0.633483,2.80991,0.576517,0.7614,1.51002,0.476467,0.442329,0.692434,2.33456,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,1.56752,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,2.27949,2.86517,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,3.27965,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.992915
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,0.612053,0.688265,0.483253,0.704257,1.88411,0.370124,1.76086,0.162942,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,1.50428,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.854272,0.503207,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.66772,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,3.2365,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,1.4408,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,1.75347,0.580757,0.57247,0.633483,2.80991,0.576517,0.7614,1.51002,0.476467,0.442329,0.692434,2.33456,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,1.56752,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,2.27949,2.86517,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,3.27965,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.992915
|tfbs_overrepresentation_jaspar=MA0003.1;1.34944,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.581929,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;1.73541,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;2.80216,MA0058.1;1.4226,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;1.94802,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;8.63716,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;1.1032,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;1.29026,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.841866,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.21199,MA0146.1;0.313734,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.45096,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,MA0155.1;1.21457,MA0156.1;0.549102,MA0157.1;2.30294,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.346529,MA0163.1;3.61171,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;9.08066,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 14:00, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126778639..126778670,-p3@Gli1
Mm9::chr10:126778916..126778974,-p1@Gli1
Mm9::chr10:126779021..126779032,-p2@Gli1
Mm9::chr13:63674708..63674738,-p1@Ptch1


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:0007224smoothened signaling pathway0.000383498602969375
GO:0009953dorsal/ventral pattern formation0.000458067775768976
GO:0048732gland development0.000913430094021413
GO:0003002regionalization0.00272177480718542
GO:0043109regulation of smoothened activity0.00291319800441589
GO:0048598embryonic morphogenesis0.00291319800441589
GO:0035295tube development0.00291319800441589
GO:0007389pattern specification process0.00336672667248463
GO:0007418ventral midline development0.00336672667248463
GO:0005113patched binding0.00336672667248463
GO:0060032notochord regression0.00336672667248463
GO:0060033anatomical structure regression0.00462912235634527
GO:0048570notochord morphogenesis0.00529028061488478
GO:0021938smoothened signaling pathway in regulation of granule cell precursor cell proliferation0.00529028061488478
GO:0009790embryonic development0.0067420677676526
GO:0021937Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation0.00685664389347801
GO:0009887organ morphogenesis0.00685664389347801
GO:0030903notochord development0.00685664389347801
GO:0015485cholesterol binding0.00685664389347801
GO:0008158hedgehog receptor activity0.00685664389347801
GO:0040015negative regulation of multicellular organism growth0.00685664389347801
GO:0021940positive regulation of granule cell precursor proliferation0.00685664389347801
GO:0021936regulation of granule cell precursor proliferation0.00685664389347801
GO:0021534cell proliferation in hindbrain0.00685664389347801
GO:0009954proximal/distal pattern formation0.00685664389347801
GO:0021924cell proliferation in the external granule layer0.00685664389347801
GO:0021930granule cell precursor proliferation0.00685664389347801
GO:0007399nervous system development0.00690808382009827
GO:0008589regulation of smoothened signaling pathway0.00766010646861597
GO:0032934sterol binding0.00835976554417887
GO:0021696cerebellar cortex morphogenesis0.00835976554417887
GO:0021587cerebellum morphogenesis0.0086767510059229
GO:0021575hindbrain morphogenesis0.00897449448372583
GO:0021695cerebellar cortex development0.00951885273914528
GO:0021983pituitary gland development0.00951885273914528
GO:0021536diencephalon development0.010282147655304
GO:0048562embryonic organ morphogenesis0.0105041764495005
GO:0030879mammary gland development0.0106411477768241
GO:0022037metencephalon development0.0106411477768241
GO:0021549cerebellum development0.0106411477768241
GO:0045926negative regulation of growth0.0112837374470277
GO:0009653anatomical structure morphogenesis0.0148410287656804
GO:0048568embryonic organ development0.0159179525336601
GO:0030902hindbrain development0.0176559464142327
GO:0008017microtubule binding0.0184936621275853
GO:0005496steroid binding0.0184936621275853
GO:0048513organ development0.0184936621275853
GO:0035270endocrine system development0.0184936621275853
GO:0040014regulation of multicellular organism growth0.0195162687051387
GO:0001841neural tube formation0.0195162687051387
GO:0015631tubulin binding0.0195162687051387
GO:0001839neural plate morphogenesis0.0195162687051387
GO:0001840neural plate development0.0195162687051387
GO:0001838embryonic epithelial tube formation0.0195162687051387
GO:0008201heparin binding0.0196770816090132
GO:0035264multicellular organism growth0.0196770816090132
GO:0030326embryonic limb morphogenesis0.0196770816090132
GO:0035113embryonic appendage morphogenesis0.0196770816090132
GO:0030324lung development0.0196770816090132
GO:0030323respiratory tube development0.0196770816090132
GO:0021915neural tube development0.0196770816090132
GO:0016485protein processing0.0196770816090132
GO:0016331morphogenesis of embryonic epithelium0.0209617737932445
GO:0048731system development0.0209617737932445
GO:0005539glycosaminoglycan binding0.0209617737932445
GO:0035107appendage morphogenesis0.0209617737932445
GO:0035108limb morphogenesis0.0209617737932445
GO:0060173limb development0.02115589848994
GO:0048736appendage development0.02115589848994
GO:0030247polysaccharide binding0.0213804384406477
GO:0001871pattern binding0.0221178296671192
GO:0008270zinc ion binding0.0236848855557652
GO:0003682chromatin binding0.0246230452223987
GO:0048856anatomical structure development0.0246230452223987
GO:0030900forebrain development0.0246230452223987
GO:0002009morphogenesis of an epithelium0.0298689584953271
GO:0007275multicellular organismal development0.0299029695567251
GO:0046914transition metal ion binding0.0336744915261688
GO:0035239tube morphogenesis0.0341194293784279
GO:0040008regulation of growth0.0341194293784279
GO:0007166cell surface receptor linked signal transduction0.0378219578990228
GO:0008284positive regulation of cell proliferation0.0395196813844614
GO:0016563transcription activator activity0.0395196813844614
GO:0007420brain development0.0403588074381917
GO:0007283spermatogenesis0.0417053039818248
GO:0048232male gamete generation0.0417053039818248
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0417053039818248
GO:0032502developmental process0.0453064908291446
GO:0043009chordate embryonic development0.0457045477608513
GO:0009792embryonic development ending in birth or egg hatching0.0458064619401872
GO:0007417central nervous system development0.046709802065086
GO:0045893positive regulation of transcription, DNA-dependent0.0471956256633701
GO:0007276gamete generation0.0494386906563075



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
multi-cellular organism5.76e-08333


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)
MA0003.11.34944
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.581929
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.11.73541
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.12.80216
MA0058.11.4226
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.11.94802
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.18.63716
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.11.29026
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.841866
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.10.313734
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.45096
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.728853
MA0155.11.21457
MA0156.10.549102
MA0157.12.30294
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.13.61171
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.29.08066
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1876&oldid=2575271"