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|top_motifs=ATF4:2.85680065525;NFKB1_REL_RELA:2.66536368567;NFE2:2.64362051325;RUNX1..3:2.35745843937;CREB1:2.35242945088;FOXP3:2.34592995934;YY1:2.24863551857;SPI1:2.14173652768;ELF1,2,4:2.1332781533;PAX8:2.13037687951;SPIB:2.05048852573;DMAP1_NCOR{1,2}_SMARC:2.03968882624;FOS_FOS{B,L1}_JUN{B,D}:2.02298021312;ATF5_CREB3:1.97071012591;BACH2:1.94319845719;E2F1..5:1.89078151026;ETS1,2:1.80366168203;bHLH_family:1.73105221934;AIRE:1.55131967383;BPTF:1.5490618464;NFE2L1:1.53349862675;CEBPA,B_DDIT3:1.50321538871;MYB:1.43332211436;FOX{I1,J2}:1.43144550127;ELK1,4_GABP{A,B1}:1.37377044435;NR6A1:1.31051057874;SPZ1:1.14590702703;ZBTB16:1.12422053656;ALX4:1.09757812562;HMX1:1.08351097665;PAX2:1.08142713182;IRF1,2:1.04479304033;NANOG{mouse}:1.02488820534;ZNF384:0.99984725225;POU2F1..3:0.980225346876;NKX6-1,2:0.930773502097;FOXQ1:0.846169918895;ALX1:0.810186794755;NFATC1..3:0.731655883925;PITX1..3:0.723621040424;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.69265062159;TEF:0.570083206508;NKX2-2,8:0.550600197503;NFY{A,B,C}:0.517328108028;FOSL2:0.456777791308;POU1F1:0.45331485826;STAT2,4,6:0.451424728332;HLF:0.41912318479;ATF6:0.381940324197;NANOG:0.346478377017;TLX2:0.318750821894;JUN:0.284639356693;SOX17:0.283688295973;TP53:0.272451715069;ATF2:0.269152149897;HSF1,2:0.225285527733;POU5F1:0.220361360714;PPARG:0.210231479614;TFDP1:0.195327903963;NFIL3:0.185898129667;FOX{D1,D2}:0.171379165155;STAT1,3:0.134226244549;FOXD3:0.127510660731;RXR{A,B,G}:0.0880738531597;IRF7:0.0867522316963;STAT5{A,B}:0.0793051439689;AHR_ARNT_ARNT2:0.0334061216884;HES1:0.0327094548064;FOXP1:-0.0288962529215;RFX2..5_RFXANK_RFXAP:-0.0584820667946;GATA6:-0.0724569900008;SOX2:-0.0758778722496;PAX6:-0.0761248550882;CDC5L:-0.0862104931188;PBX1:-0.0894694649577;IKZF2:-0.0909029463657;NR1H4:-0.101241879685;TBX4,5:-0.110210654992;CRX:-0.157608761849;SREBF1,2:-0.164134621387;ZNF143:-0.18311240689;NRF1:-0.224025906671;GATA4:-0.224314415505;ARID5B:-0.248832252549;MEF2{A,B,C,D}:-0.272182416384;PAX4:-0.280957191827;TBP:-0.289784158771;FOXO1,3,4:-0.311012157632;FOXL1:-0.316516247562;FOXN1:-0.326869872595;RXRA_VDR{dimer}:-0.328047314119;ESRRA:-0.346241925599;RORA:-0.355292502458;HBP1_HMGB_SSRP1_UBTF:-0.377676156894;FOX{F1,F2,J1}:-0.389485869494;PRDM1:-0.418366008944;SRF:-0.430587417853;BREu{core}:-0.446108658763;RFX1:-0.451402401149;NR5A1,2:-0.469136551158;NFE2L2:-0.495819798189;CDX1,2,4:-0.502601445741;EP300:-0.507824138388;EVI1:-0.513030194067;ZIC1..3:-0.514329207482;CUX2:-0.519485345719;GFI1:-0.523977807402;ZBTB6:-0.530956310374;HOX{A4,D4}:-0.540082061935;UFEwm:-0.546794088048;EN1,2:-0.571714078885;MTF1:-0.574679947885;NKX2-3_NKX2-5:-0.585845904565;HNF4A_NR2F1,2:-0.623602784325;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.647232031121;EGR1..3:-0.664517388741;POU3F1..4:-0.696184179405;FOXA2:-0.712782856775;ONECUT1,2:-0.72415956678;HNF1A:-0.725371832235;OCT4_SOX2{dimer}:-0.730381665857;LMO2:-0.731245121309;AR:-0.742152877788;MYOD1:-0.745920015658;NFIX:-0.76897948441;PAX1,9:-0.785553943075;GLI1..3:-0.808076621792;DBP:-0.839842090652;HIF1A:-0.841293957337;NKX3-1:-0.853033797937;PDX1:-0.8837596094;HAND1,2:-0.890696100783;PAX5:-0.903441638611;PRRX1,2:-0.932261322059;ZFP161:-0.953320100752;ZEB1:-0.958613989491;SOX{8,9,10}:-0.996021691611;TFAP2{A,C}:-0.997619194716;ESR1:-1.01857960829;NHLH1,2:-1.02217448198;TGIF1:-1.02836676769;MZF1:-1.03071154477;REST:-1.03162340334;NR3C1:-1.08325061917;MTE{core}:-1.09719631182;ZNF148:-1.11121731414;MED-1{core}:-1.11931119478;VSX1,2:-1.13326888304;ZNF238:-1.14267491996;LEF1_TCF7_TCF7L1,2:-1.14322033526;POU6F1:-1.16224836048;MYFfamily:-1.17874359364;GTF2A1,2:-1.18235605706;LHX3,4:-1.21850222916;MAFB:-1.2540253085;SOX5:-1.25408935098;TFAP2B:-1.2707674374;NKX2-1,4:-1.32533200914;MYBL2:-1.34011886141;TFCP2:-1.34140545649;KLF4:-1.37171127001;GZF1:-1.38108243576;SNAI1..3:-1.38496022776;ZNF423:-1.40247096459;FOXM1:-1.40331724238;RBPJ:-1.41314005078;TOPORS:-1.41428392527;SP1:-1.41787456232;SMAD1..7,9:-1.48326500783;HOX{A5,B5}:-1.49889038875;TEAD1:-1.5120548656;RREB1:-1.51809891765;MAZ:-1.52097834738;ADNP_IRX_SIX_ZHX:-1.52200991436;NKX3-2:-1.53366787306;GCM1,2:-1.53540865903;XCPE1{core}:-1.58966065976;HOXA9_MEIS1:-1.59038513182;T:-1.60003601668;HIC1:-1.60380990775;TAL1_TCF{3,4,12}:-1.62389396156;EBF1:-1.66226613419;TLX1..3_NFIC{dimer}:-1.74110704842;GTF2I:-1.7637810002;GFI1B:-1.76971478051;PATZ1:-1.86661695199;IKZF1:-1.9014277297;TFAP4:-1.9103760625;HMGA1,2:-2.12678637526
}}
}}

Revision as of 15:18, 15 February 2012


Name:common myeloid progenitor CMP, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/8J
tissuebone marrow
dev stageNA
sexmale
age9-10weeks
cell typecommon myeloid progenitor
cell lineNA
companyNA
collaborationKitamura/Nakahara
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberrep1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA
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

CNhs12550

00
10
100
1000
1000-0.0109
1001-0.0749
1002-0.116
1003-0.102
10040
10050.0491
1006-0.159
1007-0.384
10080
1009-0.126
1010.274
10100
10110
10120
1013-0.122
1014-0.0874
1015-0.0109
1016-0.424
10170
10180
10190
1020.0933
10200
10210
1022-0.124
10230.552
10240.623
1025-0.0611
10260
1027-0.048
10280
1029-0.128
103-0.0887
10300
1031-0.911
1032-0.427
10330.0491
10340
10350
10360.527
10370
1038-0.351
1039-0.0122
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: CNhs12550

Jaspar motifP-value
MA0002.24.13101e-6
MA0003.10.519
MA0004.10.102
MA0006.10.892
MA0007.10.622
MA0009.10.303
MA0014.10.64
MA0017.10.856
MA0018.22.20543e-7
MA0019.10.859
MA0024.12.15406e-5
MA0025.10.152
MA0027.10.275
MA0028.11.2842e-7
MA0029.10.205
MA0030.10.462
MA0031.10.384
MA0035.20.855
MA0038.10.0101
MA0039.20.858
MA0040.10.0441
MA0041.10.0925
MA0042.10.328
MA0043.11.04618e-5
MA0046.14.79814e-15
MA0047.20.923
MA0048.10.00546
MA0050.12.35473e-8
MA0051.14.88554e-5
MA0052.10.734
MA0055.10.00547
MA0057.10.747
MA0058.10.0346
MA0059.10.00179
MA0060.10.694
MA0061.16.62776e-8
MA0062.23.5711e-17
MA0065.20.38
MA0066.10.253
MA0067.10.00253
MA0068.10.00638
MA0069.10.537
MA0070.10.266
MA0071.10.346
MA0072.10.848
MA0073.10.682
MA0074.10.254
MA0076.13.89232e-8
MA0077.10.396
MA0078.10.595
MA0079.20.0606
MA0080.21.07993e-12
MA0081.14.06049e-5
MA0083.10.0562
MA0084.10.162
MA0087.10.659
MA0088.10.481
MA0090.10.0106
MA0091.10.99
MA0092.10.516
MA0093.10.0872
MA0099.23.56343e-16
MA0100.16.01054e-4
MA0101.12.56929e-12
MA0102.20.00116
MA0103.10.193
MA0104.20.0269
MA0105.15.21834e-7
MA0106.10.401
MA0107.11.03351e-11
MA0108.20.259
MA0111.10.975
MA0112.20.117
MA0113.10.624
MA0114.10.277
MA0115.10.923
MA0116.10.00257
MA0117.10.117
MA0119.10.312
MA0122.10.146
MA0124.10.813
MA0125.10.0494
MA0131.10.0744
MA0135.10.0312
MA0136.11.92411e-28
MA0137.20.0114
MA0138.25.66019e-5
MA0139.10.582
MA0140.10.476
MA0141.10.955
MA0142.10.824
MA0143.10.197
MA0144.10.168
MA0145.10.43
MA0146.10.192
MA0147.10.0158
MA0148.10.88
MA0149.10.169
MA0150.14.63556e-5
MA0152.10.972
MA0153.11.23413e-4
MA0154.10.39
MA0155.10.659
MA0156.12.53741e-22
MA0157.10.345
MA0159.10.0982
MA0160.10.606
MA0162.10.483
MA0163.18.35981e-5
MA0164.10.541
MA0258.10.0979
MA0259.10.214



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: CNhs12550

Novel motifP-value
10.497
100.0484
1000.714
1010.676
1020.666
1030.616
1040.735
1050.409
1060.107
1070.996
1080.623
1090.14
110.316
1100.199
1110.427
1120.188
1130.569
1140.331
1150.654
1160.759
1172.04396e-4
1180.219
1190.731
120.84
1200.361
1210.285
1220.347
1230.166
1240.348
1250.549
1260.445
1270.741
1280.177
1290.582
138.3281e-4
1300.537
1310.361
1320.403
1330.577
1340.868
1350.528
1360.202
1370.00546
1380.791
1390.719
140.504
1400.895
1410.515
1420.915
1430.132
1440.913
1450.103
1460.514
1470.578
1480.17
1490.124
150.0423
1500.516
1510.852
1520.661
1530.351
1540.409
1550.755
1560.0983
1570.875
1580.0661
1590.535
1600.478
1610.217
1620.285
1630.215
1640.0201
1650.106
1660.198
1670.258
1680.512
1690.0938
170.803
180.462
190.478
20.0591
200.0127
210.494
220.901
230.203
240.0334
250.344
260.00346
270.348
280.736
290.0263
30.199
300.124
310.568
320.236
330.107
340.553
350.566
360.0629
370.0469
380.587
390.605
40.487
400.19
410.066
420.46
430.639
440.575
450.647
460.389
470.875
480.396
490.545
50.568
500.653
510.877
520.534
530.625
540.649
550.593
560.855
570.65
580.265
590.994
60.83
600.505
610.271
620.224
630.913
640.889
650.886
660.314
670.347
680.558
690.808
70.361
700.178
710.0197
720.18
730.0491
740.926
750.00611
760.0347
770.0728
780.127
790.712
80.181
800.872
810.892
820.251
830.0526
840.33
850.433
860.257
870.0372
880.519
890.521
90.829
900.0395
910.789
920.943
930.132
940.779
950.00223
960.938
970.883
980.716
990.194



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: CNhs12550


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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