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|top_motifs=FOXO1,3,4:3.34501352643;ATF6:2.53456618723;FOXN1:2.45349992042;MYOD1:2.16075443415;ESR1:2.04293614114;GZF1:2.04148843676;AR:1.76548146241;TP53:1.72842057351;ZEB1:1.56269773253;SNAI1..3:1.42977552075;HES1:1.41950281354;FOXQ1:1.28934848162;VSX1,2:1.00349826839;HIF1A:0.945186133869;NFE2:0.923408896786;TLX2:0.832308053164;CDX1,2,4:0.826296168074;TOPORS:0.818522020515;GLI1..3:0.798526386718;FOSL2:0.783627376323;SRF:0.77179201289;NFE2L2:0.734419007966;NKX3-2:0.712552018896;SREBF1,2:0.705164073868;NFATC1..3:0.669064016378;SOX5:0.621286037032;HAND1,2:0.6080277298;HSF1,2:0.605275974236;MAFB:0.594318713099;FOXA2:0.583229638291;NFE2L1:0.554288129127;CEBPA,B_DDIT3:0.503867159516;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.499238614786;AIRE:0.455484621662;SMAD1..7,9:0.454414314545;TBX4,5:0.445713643477;ONECUT1,2:0.443374176644;SPZ1:0.424156710348;TFAP2{A,C}:0.383638170451;BACH2:0.369304343685;TLX1..3_NFIC{dimer}:0.354036845608;TFAP4:0.333091989812;HBP1_HMGB_SSRP1_UBTF:0.332641754192;FOX{D1,D2}:0.314995865459;FOX{I1,J2}:0.282579886999;TGIF1:0.239900242836;ELK1,4_GABP{A,B1}:0.239878088383;HMX1:0.236093424298;bHLH_family:0.205375072709;RXRA_VDR{dimer}:0.204230964323;SP1:0.183038745442;GTF2I:0.16864161496;REST:0.158485441992;IRF1,2:0.157361177669;ELF1,2,4:0.152743927486;YY1:0.147406728698;FOXP3:0.128558629811;AHR_ARNT_ARNT2:0.11688164072;CREB1:0.114010455021;TEAD1:0.113967596867;ETS1,2:0.100198399859;NFY{A,B,C}:0.0728532054075;GFI1:0.0427559754551;NHLH1,2:0.0389849369154;STAT2,4,6:0.00695439830601;ADNP_IRX_SIX_ZHX:0.00284822361799;XCPE1{core}:-0.0173246606798;TBP:-0.0230872000019;NKX2-1,4:-0.0274863126061;IRF7:-0.0484269442032;ATF2:-0.0551235548125;GTF2A1,2:-0.0611315578214;DMAP1_NCOR{1,2}_SMARC:-0.0644099447345;NKX2-3_NKX2-5:-0.071614527173;ATF5_CREB3:-0.0760047455611;MYFfamily:-0.0922920536531;FOXM1:-0.108695116958;ZNF143:-0.108894506968;MEF2{A,B,C,D}:-0.117220036339;TEF:-0.118305784521;HOXA9_MEIS1:-0.120446510437;GCM1,2:-0.120584078486;PAX5:-0.12619612604;RFX2..5_RFXANK_RFXAP:-0.13484868022;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.139849692712;HIC1:-0.146469678188;GATA4:-0.150773435861;MTF1:-0.15458294875;JUN:-0.156082931136;FOS_FOS{B,L1}_JUN{B,D}:-0.176433735845;POU5F1:-0.177252484048;POU2F1..3:-0.182592479735;CDC5L:-0.199616227706;LMO2:-0.200727128333;FOX{F1,F2,J1}:-0.212437117807;MED-1{core}:-0.216189207499;EVI1:-0.217672011817;NANOG:-0.224348508769;RBPJ:-0.233349199913;GFI1B:-0.235853229762;STAT5{A,B}:-0.249191045173;MYBL2:-0.265884081752;HMGA1,2:-0.266399834772;ALX4:-0.272831251834;PAX1,9:-0.278903895424;TAL1_TCF{3,4,12}:-0.279635357667;ZNF238:-0.2892575167;PITX1..3:-0.301516851062;RFX1:-0.309278294611;RUNX1..3:-0.311476913946;NKX2-2,8:-0.315288585785;NFIX:-0.315597251226;OCT4_SOX2{dimer}:-0.318131610531;HNF1A:-0.322603769028;NFKB1_REL_RELA:-0.342633762584;ZBTB6:-0.347154912513;NKX3-1:-0.350085699908;MAZ:-0.354249454272;ARID5B:-0.358010770268;BPTF:-0.359796160936;NKX6-1,2:-0.361170851756;SOX2:-0.370600903734;ZNF148:-0.373125481125;NFIL3:-0.375394182382;PAX8:-0.376644014335;PRDM1:-0.385058316306;CRX:-0.386669341241;MYB:-0.387168350632;ZBTB16:-0.390731359612;NRF1:-0.398657595115;KLF4:-0.415329770232;LEF1_TCF7_TCF7L1,2:-0.434473261866;HNF4A_NR2F1,2:-0.445258345907;PRRX1,2:-0.453413956906;SPI1:-0.461909857514;ATF4:-0.471372198409;EGR1..3:-0.473064302153;GATA6:-0.484451784897;T:-0.485441448183;RORA:-0.489120297608;HOX{A4,D4}:-0.496432758756;TFAP2B:-0.499159372963;ZFP161:-0.51262066376;HLF:-0.525157944716;PBX1:-0.526466425393;DBP:-0.531090586168;LHX3,4:-0.555423354884;ESRRA:-0.557194233067;POU6F1:-0.566771418133;SPIB:-0.586242808084;ZIC1..3:-0.590891964279;PAX2:-0.600157575827;PDX1:-0.615676667047;UFEwm:-0.645551902156;MZF1:-0.646700427086;PATZ1:-0.655597289507;STAT1,3:-0.671113885615;IKZF1:-0.672403080929;FOXP1:-0.682177330379;BREu{core}:-0.709057816493;MTE{core}:-0.721416609718;IKZF2:-0.724966885196;RREB1:-0.743324186603;NR5A1,2:-0.762332807388;SOX17:-0.767448607122;NR3C1:-0.854141259174;NR6A1:-0.857284808561;ZNF423:-0.893301611634;PAX4:-0.894451760669;SOX{8,9,10}:-0.923651788972;EN1,2:-0.962449594147;TFDP1:-0.986598490973;TFCP2:-0.999080727554;PPARG:-1.0162674847;RXR{A,B,G}:-1.03558680976;POU1F1:-1.17727641112;FOXD3:-1.18498420876;CUX2:-1.24215676819;ALX1:-1.24288123037;EP300:-1.25159509052;FOXL1:-1.26295601359;PAX6:-1.38436752024;POU3F1..4:-1.4133605994;HOX{A5,B5}:-1.43059446315;ZNF384:-1.51547909147;E2F1..5:-1.52570150655;EBF1:-1.81016774195;NR1H4:-1.85629126019;NANOG{mouse}:-2.41849528044
}}
}}

Revision as of 15:20, 15 February 2012


Name:prostate, adult, 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/6J
tissueprostate
dev stageadult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
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

CNhs10470

00
10
100
1000
10000.236
1001-0.0275
1002-0.102
10030.0617
10040
10050
10060
1007-0.122
10080
10090.0293
101-0.0488
10100
10110
10120
10130.767
1014-0.0874
1015-0.242
1016-0.204
10170
10180.0865
10190
1020
10200
10210
10220.444
10230
1024-0.0325
10250
10260.0571
10270
10280
1029-0.0282
103-0.0735
10300
1031-0.222
10320.0369
10330
10340.221
10350
1036-0.134
10370.159
1038-0.066
10390.0111
1040
10400.0169
10410.221



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: CNhs10470

Jaspar motifP-value
MA0002.20.145
MA0003.10.463
MA0004.10.517
MA0006.10.279
MA0007.10.0682
MA0009.10.798
MA0014.10.0381
MA0017.10.0725
MA0018.20.183
MA0019.10.788
MA0024.15.8711e-11
MA0025.10.566
MA0027.10.593
MA0028.10.82
MA0029.10.265
MA0030.10.449
MA0031.18.60478e-5
MA0035.20.0881
MA0038.10.671
MA0039.20.0718
MA0040.10.473
MA0041.10.583
MA0042.10.812
MA0043.10.174
MA0046.17.47149e-4
MA0047.25.97569e-8
MA0048.10.324
MA0050.10.119
MA0051.10.0206
MA0052.10.931
MA0055.10.301
MA0057.10.171
MA0058.10.531
MA0059.10.611
MA0060.10.317
MA0061.10.0745
MA0062.20.863
MA0065.20.402
MA0066.10.589
MA0067.10.422
MA0068.10.184
MA0069.10.71
MA0070.10.294
MA0071.10.776
MA0072.10.724
MA0073.10.992
MA0074.10.772
MA0076.10.495
MA0077.10.419
MA0078.10.695
MA0079.20.277
MA0080.20.658
MA0081.10.151
MA0083.10.0238
MA0084.10.977
MA0087.10.348
MA0088.10.0559
MA0090.10.947
MA0091.10.194
MA0092.10.716
MA0093.10.62
MA0099.20.00811
MA0100.10.742
MA0101.10.0999
MA0102.20.497
MA0103.15.20546e-7
MA0104.20.681
MA0105.10.0103
MA0106.10.358
MA0107.10.102
MA0108.20.937
MA0111.10.202
MA0112.20.0139
MA0113.10.0982
MA0114.10.0407
MA0115.10.136
MA0116.10.78
MA0117.10.0711
MA0119.10.382
MA0122.10.777
MA0124.10.0325
MA0125.10.857
MA0131.10.476
MA0135.10.852
MA0136.10.129
MA0137.20.00428
MA0138.20.0357
MA0139.10.138
MA0140.10.693
MA0141.10.221
MA0142.10.432
MA0143.10.18
MA0144.19.48971e-7
MA0145.10.0942
MA0146.10.333
MA0147.10.73
MA0148.16.52316e-5
MA0149.10.0774
MA0150.10.00249
MA0152.10.645
MA0153.10.00103
MA0154.10.96
MA0155.10.566
MA0156.10.221
MA0157.14.00612e-4
MA0159.10.329
MA0160.10.626
MA0162.10.714
MA0163.10.402
MA0164.10.727
MA0258.10.135
MA0259.10.868



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: CNhs10470

Novel motifP-value
10.316
100.661
1000.765
1010.646
1020.222
1030.109
1040.574
1050.905
1060.0213
1070.747
1080.72
1090.123
110.41
1100.448
1110.0195
1120.148
1130.498
1140.338
1150.507
1160.654
1170.887
1180.0813
1190.00402
120.377
1200.596
1210.321
1220.858
1230.727
1240.0124
1250.805
1260.453
1270.773
1280.228
1290.23
130.0835
1300.395
1310.473
1320.15
1330.958
1340.834
1350.272
1360.311
1370.768
1380.145
1390.387
140.882
1400.184
1410.608
1420.758
1430.603
1440.335
1450.173
1460.0781
1470.175
1480.207
1490.362
150.422
1500.158
1510.0757
1520.0225
1530.467
1540.407
1550.0988
1560.0085
1570.707
1580.559
1590.274
1600.961
1610.105
1620.912
1630.764
1640.275
1650.11
1660.781
1670.5
1680.761
1690.0768
170.0163
180.426
190.0595
20.267
200.327
210.112
220.153
230.37
240.015
250.6
260.132
270.254
280.73
290.138
30.812
300.55
310.461
320.223
330.945
340.167
350.494
360.358
370.0454
380.529
390.309
40.849
400.398
410.827
420.992
430.41
440.457
450.604
460.201
470.381
480.253
490.409
50.137
500.606
510.959
520.137
530.805
540.953
550.568
560.635
570.241
580.228
590.454
60.358
600.0911
610.869
620.418
630.157
640.854
650.307
660.962
670.177
680.0923
690.0635
70.568
700.00341
710.373
720.381
730.00929
740.337
750.447
760.131
770.273
780.64
790.722
80.919
800.96
810.736
820.0665
830.229
840.0647
850.0122
860.171
870.177
880.502
890.104
90.92
900.741
910.189
920.863
930.0326
940.955
950.648
960.0285
970.0146
980.513
990.839



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: CNhs10470


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

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000079 (male reproductive system)
0000119 (cell layer)
0000161 (orifice)
0000162 (cloaca)
0000163 (embryonic cloaca)
0000164 (primitive urogenital sinus)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000990 (reproductive system)
0001007 (digestive system)
0001046 (hindgut)
0001062 (anatomical entity)
0001353 (anal region)
0001555 (digestive tract)
0002050 (embryonic structure)
0002367 (prostate gland)
0002530 (gland)
0002532 (epiblast (generic))
0003064 (intermediate mesoderm)
0003101 (male organism)
0003104 (mesenchyme)
0003353 (epithelium of hindgut)
0003820 (prostate bud)
0003929 (gut epithelium)
0003937 (sex gland)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004122 (genitourinary system)
0004185 (endodermal part of digestive tract)
0004902 (urogenital sinus epithelium)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005156 (reproductive structure)
0005291 (embryonic tissue)
0005399 (male reproductive gland)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006866 (terminal part of digestive tract)
0007023 (adult organism)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

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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