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MCL coexpression mm9:347: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000055!2.98e-19!49;CL:0000221!9.81e-18!44;CL:0000133!9.81e-18!44;CL:0002319!2.39e-17!43;CL:0000393!1.18e-14!39;CL:0000211!1.18e-14!39;CL:0000540!7.32e-13!33;CL:0000047!7.32e-13!33;CL:0000031!7.32e-13!33;CL:0000404!7.32e-13!33;CL:0000117!1.84e-12!23;CL:0000337!1.84e-12!23;CL:0002321!5.69e-11!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.82e-34!73;UBERON:0001016!3.64e-34!75;UBERON:0010314!9.32e-30!92;UBERON:0004121!9.91e-29!95;UBERON:0000924!9.91e-29!95;UBERON:0006601!9.91e-29!95;UBERON:0000073!6.58e-28!54;UBERON:0001049!2.41e-26!52;UBERON:0005068!2.41e-26!52;UBERON:0006241!2.41e-26!52;UBERON:0007135!2.41e-26!52;UBERON:0002346!9.64e-26!64;UBERON:0003075!9.64e-26!64;UBERON:0007284!9.64e-26!64;UBERON:0000955!6.79e-23!47;UBERON:0006238!6.79e-23!47;UBERON:0002616!1.94e-22!46;UBERON:0010371!2.75e-22!73;UBERON:0002020!3.03e-19!34;UBERON:0003080!4.91e-19!40;UBERON:0002780!1.90e-18!39;UBERON:0001890!1.90e-18!39;UBERON:0006240!1.90e-18!39;UBERON:0003056!2.09e-18!49;UBERON:0003528!4.00e-16!29;UBERON:0002791!4.00e-16!29;UBERON:0001893!4.00e-16!29;UBERON:0000025!1.75e-14!114;UBERON:0004111!2.97e-14!122;UBERON:0000956!6.93e-12!21;UBERON:0001869!6.93e-12!21;UBERON:0000203!6.93e-12!21;UBERON:0002619!1.71e-10!17;UBERON:0003076!7.67e-08!12;UBERON:0003057!7.67e-08!12;UBERON:0002021!1.08e-07!10;UBERON:0000411!1.08e-07!10;UBERON:0001950!1.08e-07!10
|tfbs_overrepresentation_for_novel_motifs=1.81543,0.470303,1.68703,0.144583,0.0514566,0.15366,0.615468,0.436916,0.247005,1.51667,2.32892,0.206436,1.43948,0.636202,0.211839,0,0.374352,0.0483719,0.393073,1.00488,0.604268,0.495413,0.63467,0.0508498,0.715008,1.26705,0.0157515,0.167184,0.53096,1.70353,0.477864,0.460285,1.09732,0.809053,2.26244,0.654385,0.680806,0.589223,0.608153,0.515604,0.0498798,0.486105,0.161515,0.214332,3.11273,0.843029,1.5084,1.00921,0.0553373,0.252327,1.6861,0.729809,0.932451,0.586014,1.46504,1.21039,0.559359,0.573993,0.575924,1.20474,1.127,0.746278,0.269556,0.92519,1.2413,0.384144,0.727642,1.06142,0.438956,0.919268,1.59481,0.0971174,2.03698,0.632466,1.5474,0.769781,0.157028,0.300684,0.428247,0.614637,0.0226705,1.78624,0.270104,0.217876,1.3095,3.68353,0.123224,0.255395,0.842295,1.21975,0.793151,0.532634,0.471416,0.198642,0.934714,0.122418,0.0897681,0.473864,0.309859,0.204213,0.0440835,0.460042,0.570262,0.946715,0.359547,1.5038,1.05419,0.174935,0.626635,0.608663,0.744411,0.57187,0.0881503,1.65852,0.799811,0.184628,2.26242,0.450125,0.979825,0.374781,0.637418,0.333667,0.245224,0.299972,0.851175,0.43141,0.220786,0.465518,0.726225,0.446029,0.554981,0.432886,0.698665,0.238902,0.820264,0.0929961,0.78425,0.488358,0.773792,1.58317,1.18855,0.732048,0.254204,0.469382,1.66621,0.944018,0.31213,1.54387,0.125637,0.753189,0.261373,1.7765,0.587436,1.27075,0.238221,0.662158,0.264789,1.28124,0.117954,1.27697,0.782756,0.527439,0.431791,0.365959,0.351524,0.232792,0.380389,0.205322,1.69268
|tfbs_overrepresentation_jaspar=MA0003.1;2.89686,MA0004.1;1.40666,MA0006.1;0.2064,MA0007.1;1.35014,MA0009.1;0.483331,MA0014.1;2.93197,MA0017.1;0.515383,MA0019.1;0.329708,MA0024.1;1.13202,MA0025.1;0.694475,MA0027.1;2.07936,MA0028.1;1.7477,MA0029.1;0.426655,MA0030.1;0.43227,MA0031.1;0.402033,MA0038.1;0.243815,MA0040.1;0.494317,MA0041.1;2.91576,MA0042.1;2.17282,MA0043.1;0.569356,MA0046.1;0.514989,MA0048.1;2.32441,MA0050.1;0.506524,MA0051.1;0.698522,MA0052.1;0.501416,MA0055.1;0.630035,MA0056.1;0,MA0057.1;0.327386,MA0058.1;2.13126,MA0059.1;1.09596,MA0060.1;1.20594,MA0061.1;0.343057,MA0063.1;0,MA0066.1;0.664275,MA0067.1;0.798606,MA0068.1;0.341633,MA0069.1;1.25311,MA0070.1;0.493176,MA0071.1;0.169125,MA0072.1;0.485733,MA0073.1;0.070907,MA0074.1;0.209912,MA0076.1;0.950765,MA0077.1;0.466808,MA0078.1;0.275441,MA0081.1;0.717402,MA0083.1;1.39512,MA0084.1;1.11388,MA0087.1;0.530004,MA0088.1;0.512673,MA0089.1;0,MA0090.1;0.124244,MA0091.1;0.465605,MA0092.1;0.39292,MA0093.1;2.3643,MA0095.1;0,MA0098.1;0,MA0100.1;0.201797,MA0101.1;1.65933,MA0103.1;0.253989,MA0105.1;0.515449,MA0106.1;1.40621,MA0107.1;0.899134,MA0108.2;0.348212,MA0109.1;0,MA0111.1;0.413949,MA0113.1;1.32697,MA0114.1;0.145706,MA0115.1;0.571881,MA0116.1;0.788841,MA0117.1;0.542889,MA0119.1;0.101951,MA0122.1;0.560692,MA0124.1;0.748494,MA0125.1;0.67944,MA0130.1;0,MA0131.1;0.326061,MA0132.1;0,MA0133.1;0,MA0135.1;0.602346,MA0136.1;0.637057,MA0139.1;1.02435,MA0140.1;0.201717,MA0141.1;0.0822433,MA0142.1;0.389844,MA0143.1;0.27232,MA0144.1;0.621329,MA0145.1;0.799315,MA0146.1;5.54819,MA0147.1;0.662138,MA0148.1;0.155077,MA0149.1;0.104621,MA0062.2;2.91081,MA0035.2;0.205003,MA0039.2;2.73775,MA0138.2;0.319705,MA0002.2;0.227684,MA0137.2;0.276466,MA0104.2;1.12358,MA0047.2;0.243248,MA0112.2;1.73464,MA0065.2;0.373593,MA0150.1;0.421594,MA0151.1;0,MA0152.1;0.243327,MA0153.1;0.617506,MA0154.1;0.201776,MA0155.1;0.267894,MA0156.1;0.558833,MA0157.1;0.363212,MA0158.1;0,MA0159.1;0.0457298,MA0160.1;0.156994,MA0161.1;0,MA0162.1;0.649913,MA0163.1;2.766,MA0164.1;0.637671,MA0080.2;0.247073,MA0018.2;1.89645,MA0099.2;0.314682,MA0079.2;1.34269,MA0102.2;1.16504,MA0258.1;0.895773,MA0259.1;0.978746,MA0442.1;0
}}

Latest revision as of 15:08, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:77441365..77441416,+p1@1810043G02Rik
Mm9::chr11:59661542..59661604,+p1@Nt5m
Mm9::chr15:76490121..76490173,-p2@Cyhr1
Mm9::chr15:99556129..99556143,+p5@2310016M24Rik
Mm9::chr15:99556151..99556168,+p3@2310016M24Rik
Mm9::chr16:35769447..35769470,-p1@Dirc2
Mm9::chr17:25922478..25922536,-p1@Haghl
Mm9::chr17:26078871..26078926,-p1@Pigq
Mm9::chr19:46403193..46403258,+p@chr19:46403193..46403258
+
Mm9::chr19:5038847..5038938,+p1@B3gnt1
Mm9::chr19:5457488..5457494,-p2@Ccdc85b
Mm9::chr19:5457504..5457573,-p1@Ccdc85b
Mm9::chr1:167391321..167391370,+p2@Brp44
Mm9::chr2:130275995..130276045,+p1@Ptpra
Mm9::chr2:155102154..155102210,+p1@Map1lc3a
Mm9::chr2:32237429..32237440,-p2@1110008P14Rik
Mm9::chr5:104475937..104475994,+p1@Nudt9
Mm9::chr5:136108566..136108597,+p1@Rhbdd2
Mm9::chr7:150238657..150238668,+p2@Cd81
Mm9::chr7:16683923..16683934,+p2@Napa
Mm9::chr7:26101936..26101987,+p3@Megf8
Mm9::chr9:58100982..58101079,+p1@Stoml1


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

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
central nervous system2.82e-3473
nervous system3.64e-3475
structure with developmental contribution from neural crest9.32e-3092
ectoderm-derived structure9.91e-2995
ectoderm9.91e-2995
presumptive ectoderm9.91e-2995
regional part of nervous system6.58e-2854
neural tube2.41e-2652
neural rod2.41e-2652
future spinal cord2.41e-2652
neural keel2.41e-2652
neurectoderm9.64e-2664
neural plate9.64e-2664
presumptive neural plate9.64e-2664
brain6.79e-2347
future brain6.79e-2347
regional part of brain1.94e-2246
ecto-epithelium2.75e-2273
gray matter3.03e-1934
anterior neural tube4.91e-1940
regional part of forebrain1.90e-1839
forebrain1.90e-1839
future forebrain1.90e-1839
pre-chordal neural plate2.09e-1849
brain grey matter4.00e-1629
regional part of telencephalon4.00e-1629
telencephalon4.00e-1629
tube1.75e-14114
anatomical conduit2.97e-14122
cerebral cortex6.93e-1221
cerebral hemisphere6.93e-1221
pallium6.93e-1221
regional part of cerebral cortex1.71e-1017
posterior neural tube7.67e-0812
chordal neural plate7.67e-0812
occipital lobe1.08e-0710
visual cortex1.08e-0710
neocortex1.08e-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)
MA0003.12.89686
MA0004.11.40666
MA0006.10.2064
MA0007.11.35014
MA0009.10.483331
MA0014.12.93197
MA0017.10.515383
MA0019.10.329708
MA0024.11.13202
MA0025.10.694475
MA0027.12.07936
MA0028.11.7477
MA0029.10.426655
MA0030.10.43227
MA0031.10.402033
MA0038.10.243815
MA0040.10.494317
MA0041.12.91576
MA0042.12.17282
MA0043.10.569356
MA0046.10.514989
MA0048.12.32441
MA0050.10.506524
MA0051.10.698522
MA0052.10.501416
MA0055.10.630035
MA0056.10
MA0057.10.327386
MA0058.12.13126
MA0059.11.09596
MA0060.11.20594
MA0061.10.343057
MA0063.10
MA0066.10.664275
MA0067.10.798606
MA0068.10.341633
MA0069.11.25311
MA0070.10.493176
MA0071.10.169125
MA0072.10.485733
MA0073.10.070907
MA0074.10.209912
MA0076.10.950765
MA0077.10.466808
MA0078.10.275441
MA0081.10.717402
MA0083.11.39512
MA0084.11.11388
MA0087.10.530004
MA0088.10.512673
MA0089.10
MA0090.10.124244
MA0091.10.465605
MA0092.10.39292
MA0093.12.3643
MA0095.10
MA0098.10
MA0100.10.201797
MA0101.11.65933
MA0103.10.253989
MA0105.10.515449
MA0106.11.40621
MA0107.10.899134
MA0108.20.348212
MA0109.10
MA0111.10.413949
MA0113.11.32697
MA0114.10.145706
MA0115.10.571881
MA0116.10.788841
MA0117.10.542889
MA0119.10.101951
MA0122.10.560692
MA0124.10.748494
MA0125.10.67944
MA0130.10
MA0131.10.326061
MA0132.10
MA0133.10
MA0135.10.602346
MA0136.10.637057
MA0139.11.02435
MA0140.10.201717
MA0141.10.0822433
MA0142.10.389844
MA0143.10.27232
MA0144.10.621329
MA0145.10.799315
MA0146.15.54819
MA0147.10.662138
MA0148.10.155077
MA0149.10.104621
MA0062.22.91081
MA0035.20.205003
MA0039.22.73775
MA0138.20.319705
MA0002.20.227684
MA0137.20.276466
MA0104.21.12358
MA0047.20.243248
MA0112.21.73464
MA0065.20.373593
MA0150.10.421594
MA0151.10
MA0152.10.243327
MA0153.10.617506
MA0154.10.201776
MA0155.10.267894
MA0156.10.558833
MA0157.10.363212
MA0158.10
MA0159.10.0457298
MA0160.10.156994
MA0161.10
MA0162.10.649913
MA0163.12.766
MA0164.10.637671
MA0080.20.247073
MA0018.21.89645
MA0099.20.314682
MA0079.21.34269
MA0102.21.16504
MA0258.10.895773
MA0259.10.978746
MA0442.10
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