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|top_motifs=IRF7:3.09373837861;POU2F1..3:3.05425788507;GATA6:2.85339698398;E2F1..5:1.70483330436;POU5F1:1.59871962823;PPARG:1.39063904264;YY1:1.35061421991;STAT5{A,B}:1.32966311405;SPIB:1.27504408986;AIRE:1.1717714913;MYB:1.16092728604;RUNX1..3:1.08841431467;NFE2L2:1.04990136101;IRF1,2:1.01931469819;bHLH_family:0.906080955487;PITX1..3:0.903735432235;ZBTB16:0.885405508983;PAX1,9:0.877981869394;ETS1,2:0.875401660726;SPI1:0.872276445156;NFKB1_REL_RELA:0.83473270926;DMAP1_NCOR{1,2}_SMARC:0.83133268051;ELF1,2,4:0.794402960476;POU1F1:0.765260259497;ALX4:0.709544975147;NFE2L1:0.639447185847;OCT4_SOX2{dimer}:0.638809805609;NFY{A,B,C}:0.610123968947;PAX8:0.588871039823;TEF:0.570877896714;HES1:0.543630739923;ARID5B:0.491533000527;PBX1:0.483293743511;CEBPA,B_DDIT3:0.477108314321;PAX2:0.459107262015;ATF5_CREB3:0.396903650633;HOX{A5,B5}:0.385555762945;ELK1,4_GABP{A,B1}:0.373076651577;ATF4:0.364570864151;PDX1:0.344570853974;NFE2:0.305207182558;ZNF423:0.297112997036;HOXA9_MEIS1:0.288115527797;TFDP1:0.251556534408;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.220592154276;NKX2-2,8:0.220557056839;NR6A1:0.198880744897;TLX2:0.19468438399;FOXP3:0.189628742988;STAT2,4,6:0.145529207985;SOX17:0.0333554845868;TAL1_TCF{3,4,12}:0.012911711868;FOX{F1,F2,J1}:-0.030266127234;CDX1,2,4:-0.149231069033;HLF:-0.151904885697;FOX{D1,D2}:-0.165039985719;FOXP1:-0.183778672378;NRF1:-0.192049054902;ZNF143:-0.192508147299;RXRA_VDR{dimer}:-0.203786474653;RFX2..5_RFXANK_RFXAP:-0.215121624074;TBX4,5:-0.220271118308;ALX1:-0.245031471546;FOX{I1,J2}:-0.251693147129;BACH2:-0.272611440528;BPTF:-0.289211840388;STAT1,3:-0.291380608359;FOXM1:-0.309805390093;FOXL1:-0.313335162479;FOXO1,3,4:-0.321870322812;HSF1,2:-0.32798042293;LMO2:-0.340867257787;GLI1..3:-0.343180562364;SOX{8,9,10}:-0.36570812605;GFI1:-0.372819193312;SREBF1,2:-0.384153782108;CREB1:-0.408375233227;NR5A1,2:-0.425173480733;AHR_ARNT_ARNT2:-0.425679896173;CRX:-0.427785554871;NANOG{mouse}:-0.429259912383;HOX{A4,D4}:-0.446465073551;ZEB1:-0.449129831821;BREu{core}:-0.454359484603;NFIX:-0.469252258534;NANOG:-0.471395405067;PRRX1,2:-0.525754529779;POU6F1:-0.532454651187;FOXA2:-0.536770727589;NKX3-1:-0.543484418115;ADNP_IRX_SIX_ZHX:-0.559748888651;EBF1:-0.573065486316;TGIF1:-0.574338499955;NFATC1..3:-0.579555328248;FOXQ1:-0.603745389406;MEF2{A,B,C,D}:-0.603823509827;PAX4:-0.618303122397;NR1H4:-0.627532992739;HNF4A_NR2F1,2:-0.634530434428;PRDM1:-0.650522220092;NKX6-1,2:-0.66578790749;HNF1A:-0.666007178988;RFX1:-0.679954201119;FOS_FOS{B,L1}_JUN{B,D}:-0.70353236757;EVI1:-0.71320594277;TBP:-0.722085305249;IKZF2:-0.746558238141;ZBTB6:-0.781290049997;SNAI1..3:-0.788106138587;NKX3-2:-0.792856739423;SMAD1..7,9:-0.797895358187;ZFP161:-0.80055391442;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.817750528072;UFEwm:-0.824492557234;CDC5L:-0.843089304611;RORA:-0.850065851787;PAX6:-0.855617966227;NHLH1,2:-0.862198128203;ATF2:-0.863711673696;MYFfamily:-0.864437698298;VSX1,2:-0.868107653453;NFIL3:-0.870777190987;ZNF148:-0.874970480627;IKZF1:-0.8882260009;JUN:-0.894578710015;MYOD1:-0.904900484301;TP53:-0.938136868857;LHX3,4:-0.971738611784;MTF1:-0.973291418544;EGR1..3:-0.9777095669;SRF:-0.996281542778;MAFB:-1.0177828695;ZNF384:-1.01799651977;AR:-1.02185841324;ESRRA:-1.02200283473;NKX2-1,4:-1.02854819443;GATA4:-1.0316703633;TOPORS:-1.0347360526;SOX2:-1.03530519476;HMGA1,2:-1.03693645226;REST:-1.06203899465;GZF1:-1.07942401769;ONECUT1,2:-1.08525874774;SPZ1:-1.09578182427;GCM1,2:-1.13017421256;MED-1{core}:-1.1323934931;POU3F1..4:-1.14103609114;CUX2:-1.14738561072;MYBL2:-1.17897411029;HAND1,2:-1.18434560372;FOXD3:-1.19084485261;RREB1:-1.21477057443;HIF1A:-1.24158449913;TFAP2{A,C}:-1.24967187237;HBP1_HMGB_SSRP1_UBTF:-1.2529634315;KLF4:-1.27374761669;MZF1:-1.28618663548;SOX5:-1.29904403822;XCPE1{core}:-1.30430125602;TFAP2B:-1.30466156687;RXR{A,B,G}:-1.31471092894;NKX2-3_NKX2-5:-1.34809607528;MTE{core}:-1.37546182311;EP300:-1.381301244;TLX1..3_NFIC{dimer}:-1.38378834987;NR3C1:-1.3844216095;ESR1:-1.39061096285;TEAD1:-1.40010200503;ZNF238:-1.41654066449;LEF1_TCF7_TCF7L1,2:-1.4178412429;EN1,2:-1.49333269411;HMX1:-1.49426455999;PATZ1:-1.49464830052;HIC1:-1.49635093886;ZIC1..3:-1.51057793001;T:-1.59581222123;TFCP2:-1.62745145992;GTF2A1,2:-1.631651659;PAX5:-1.6424055913;FOSL2:-1.69424528244;GFI1B:-1.7303329056;FOXN1:-1.75824335891;DBP:-1.77253216639;TFAP4:-1.77401841412;ATF6:-1.79788096483;GTF2I:-1.80202248775;MAZ:-1.83665510687;RBPJ:-1.85138149909;SP1:-2.0185061562
}}
}}

Revision as of 15:16, 15 February 2012


Name:CD41+ megakaryocyte cancer, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemegakaryocyte
cell lineNA
companyNA
collaborationHozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3LL-1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs13079

00
10
100
1000
10000
1001-0.0749
1002-0.116
1003-0.175
10040
10050
1006-0.143
1007-0.253
10080
1009-0.19
1010.118
10100
1011-0.108
10120
1013-0.131
1014-0.0874
1015-0.202
1016-0.442
10170
10180
10190
1020
10200.368
10210.564
1022-0.0704
10230
1024-0.307
1025-0.0611
10260
1027-0.048
10280
1029-0.115
103-0.0861
10300.125
1031-0.677
1032-0.287
10330.0509
10340
10350
10360.365
10370
1038-0.267
1039-0.253
1040
1040-0.216
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13079

Jaspar motifP-value
MA0002.26.64238e-4
MA0003.10.587
MA0004.10.34
MA0006.10.651
MA0007.10.987
MA0009.10.785
MA0014.10.961
MA0017.10.0746
MA0018.20.254
MA0019.10.382
MA0024.12.55182e-5
MA0025.10.413
MA0027.10.48
MA0028.10.00739
MA0029.10.677
MA0030.10.255
MA0031.10.778
MA0035.26.60589e-5
MA0038.10.48
MA0039.20.922
MA0040.10.623
MA0041.10.804
MA0042.10.996
MA0043.10.0666
MA0046.16.01759e-6
MA0047.20.875
MA0048.10.162
MA0050.12.52639e-5
MA0051.17.09848e-4
MA0052.11.33854e-4
MA0055.10.0627
MA0057.10.668
MA0058.10.351
MA0059.10.045
MA0060.10.655
MA0061.10.00606
MA0062.24.5605e-6
MA0065.20.0715
MA0066.10.0973
MA0067.10.721
MA0068.10.726
MA0069.10.372
MA0070.10.351
MA0071.10.604
MA0072.10.932
MA0073.10.841
MA0074.10.669
MA0076.10.034
MA0077.10.402
MA0078.10.605
MA0079.20.0215
MA0080.21.96472e-9
MA0081.10.036
MA0083.10.00593
MA0084.10.48
MA0087.10.315
MA0088.10.183
MA0090.10.0363
MA0091.10.224
MA0092.10.967
MA0093.10.422
MA0099.20.823
MA0100.10.0215
MA0101.10.0123
MA0102.20.695
MA0103.10.647
MA0104.20.151
MA0105.13.98226e-5
MA0106.10.509
MA0107.10.0304
MA0108.20.00179
MA0111.10.841
MA0112.20.00896
MA0113.10.208
MA0114.10.448
MA0115.10.329
MA0116.10.00411
MA0117.10.675
MA0119.10.428
MA0122.10.854
MA0124.10.966
MA0125.10.0469
MA0131.10.565
MA0135.10.0758
MA0136.15.81896e-8
MA0137.20.339
MA0138.20.0157
MA0139.10.492
MA0140.13.23797e-24
MA0141.10.107
MA0142.10.025
MA0143.10.305
MA0144.10.561
MA0145.10.582
MA0146.10.203
MA0147.10.0773
MA0148.10.91
MA0149.10.0296
MA0150.10.00334
MA0152.10.261
MA0153.18.14128e-4
MA0154.10.0104
MA0155.10.332
MA0156.19.2405e-7
MA0157.10.906
MA0159.10.0281
MA0160.10.253
MA0162.10.358
MA0163.11.28917e-4
MA0164.10.415
MA0258.10.0508
MA0259.10.379



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13079

Novel motifP-value
10.0842
100.0214
1000.544
1010.878
1020.728
1030.00925
1040.952
1050.931
1060.257
1070.92
1080.797
1090.0678
110.131
1100.0574
1110.021
1120.0484
1130.755
1140.334
1150.626
1160.747
1173.26204e-4
1180.0921
1190.472
120.729
1200.71
1210.297
1220.938
1230.274
1240.545
1250.103
1260.204
1270.304
1280.287
1290.216
130.0252
1300.962
1310.866
1320.164
1330.92
1340.218
1350.443
1360.983
1370.214
1380.573
1390.237
140.92
1400.566
1410.728
1420.464
1430.106
1440.977
1450.0289
1460.898
1470.813
1480.203
1490.324
150.0409
1500.248
1510.214
1520.577
1530.673
1540.833
1550.183
1562.32464e-53
1570.919
1580.0236
1590.66
1600.601
1610.0282
1620.581
1630.627
1640.0465
1650.409
1660.177
1670.173
1680.896
1690.181
170.424
180.117
190.821
20.232
200.0355
210.336
220.779
230.464
240.452
250.198
260.0116
270.633
280.35
290.0183
30.046
300.483
310.807
320.928
330.182
340.984
350.245
360.0235
370.158
380.976
390.789
40.965
400.179
410.414
420.0766
430.152
440.321
450.693
460.161
470.135
480.195
490.0691
50.00858
500.799
510.874
520.954
530.663
540.936
550.197
560.619
570.259
580.288
590.309
60.713
600.418
610.357
620.115
630.505
640.5
650.944
660.423
670.46
680.0683
690.871
70.0814
700.159
710.0147
720.286
730.25
740.739
750.0154
760.0651
770.869
780.0441
790.704
80.0231
800.0401
810.45
820.536
830.225
840.571
850.252
860.555
870.564
880.546
890.828
90.937
900.0276
910.182
920.313
930.257
940.116
950.0835
960.129
970.836
980.161
990.712



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs13079


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000050 (megakaryocyte-erythroid progenitor cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000553 (megakaryocyte progenitor cell)
0000556 (megakaryocyte)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0002006 (Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell)
0002024 (Kit-positive megakaryocyte progenitor cell)
0002027 (CD9-positive, CD41-positive megakaryocyte cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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