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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000079,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000473,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000991,UBERON:0001048,UBERON:0001062,UBERON:0001301,UBERON:0001343,UBERON:0002050,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003101,UBERON:0003133,UBERON:0003135,UBERON:0004111,UBERON:0004120,UBERON:0004176,UBERON:0004458,UBERON:0005156,UBERON:0005423,UBERON:0005564,UBERON:0005904,UBERON:0009117,UBERON:0009196
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|ancestors_in_disease_facet=
|ancestors_in_disease_facet=

Revision as of 18:01, 8 June 2012


Name:epididymis and seminiferous tubule, neonate N00
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueepididymis and seminiferous tubule
dev stage0 day neonate
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]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs11218

00
10
100
1000
10000.0435
10010.0886
10020.85
10030.188
10040.305
10050
1006-0.011
10070.141
10080
10090.331
1010.0264
10100
10110.0021
10120.0421
1013-0.141
10140.502
10150.171
10160.427
10170
10180.0421
10190
1020
10200
10210.0805
1022-0.0283
10230
10240.0585
10250.098
10260.0863
10270
10280
10290.226
1030.671
10300
10310.701
10320.0174
1033-0.0244
10340
10350
10360.0675
10370
10380.103
1039-0.102
1040
10400.31
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: CNhs11218

Jaspar motifP-value
MA0002.20.00179
MA0003.10.56
MA0004.10.466
MA0006.10.888
MA0007.10.548
MA0009.10.352
MA0014.10.246
MA0017.13.55163e-5
MA0018.20.144
MA0019.10.786
MA0024.17.96657e-4
MA0025.10.115
MA0027.10.144
MA0028.10.159
MA0029.10.628
MA0030.10.719
MA0031.10.772
MA0035.23.75903e-5
MA0038.10.275
MA0039.20.456
MA0040.10.0773
MA0041.10.0751
MA0042.10.406
MA0043.10.907
MA0046.10.0196
MA0047.20.0424
MA0048.10.147
MA0050.10.723
MA0051.10.722
MA0052.10.0679
MA0055.10.158
MA0057.10.59
MA0058.10.394
MA0059.10.167
MA0060.10.291
MA0061.10.542
MA0062.20.00281
MA0065.22.2295e-4
MA0066.10.0194
MA0067.10.276
MA0068.10.798
MA0069.10.537
MA0070.10.99
MA0071.10.00436
MA0072.15.54261e-4
MA0073.10.737
MA0074.10.755
MA0076.10.179
MA0077.10.883
MA0078.10.0578
MA0079.20.11
MA0080.22.23902e-5
MA0081.10.0416
MA0083.10.00113
MA0084.10.904
MA0087.10.351
MA0088.10.0927
MA0090.10.176
MA0091.10.605
MA0092.10.665
MA0093.10.479
MA0099.20.0252
MA0100.10.276
MA0101.10.853
MA0102.20.618
MA0103.10.00164
MA0104.20.098
MA0105.10.013
MA0106.10.775
MA0107.10.831
MA0108.20.976
MA0111.10.531
MA0112.25.97573e-4
MA0113.10.928
MA0114.15.19039e-5
MA0115.11.01068e-4
MA0116.10.0275
MA0117.10.168
MA0119.10.298
MA0122.10.403
MA0124.10.098
MA0125.10.287
MA0131.10.583
MA0135.10.863
MA0136.19.23726e-6
MA0137.20.406
MA0138.20.00503
MA0139.10.019
MA0140.10.012
MA0141.11.81188e-4
MA0142.10.0122
MA0143.10.935
MA0144.10.777
MA0145.10.333
MA0146.10.76
MA0147.10.0754
MA0148.10.0193
MA0149.10.0251
MA0150.13.90525e-4
MA0152.10.00173
MA0153.10.00721
MA0154.10.0521
MA0155.10.529
MA0156.10.0162
MA0157.10.615
MA0159.10.00129
MA0160.17.77984e-4
MA0162.10.702
MA0163.10.859
MA0164.10.905
MA0258.11.76605e-4
MA0259.10.744



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: CNhs11218

Novel motifP-value
10.0454
100.119
1000.857
1010.405
1020.997
1030.269
1040.928
1050.555
1060.445
1070.788
1080.693
1090.159
110.124
1100.24
1110.0246
1120.47
1130.644
1140.0106
1150.682
1160.945
1170.00977
1180.484
1190.0399
120.58
1200.294
1210.395
1220.705
1230.188
1240.287
1250.46
1260.409
1270.201
1280.244
1290.349
130.459
1300.468
1310.728
1320.748
1330.192
1340.754
1350.106
1360.469
1370.846
1380.0753
1390.0125
140.466
1400.434
1410.374
1420.589
1430.387
1440.189
1450.625
1460.521
1470.715
1480.574
1490.853
150.0604
1500.499
1510.0575
1520.727
1530.912
1540.669
1550.701
1560.00982
1570.681
1580.347
1590.411
1600.776
1610.55
1620.948
1630.0571
1640.539
1650.164
1660.0108
1670.292
1680.583
1690.306
170.308
180.154
190.876
20.789
200.642
210.846
220.913
230.352
240.822
250.083
260.899
270.624
280.187
290.27
30.219
300.925
310.588
320.698
330.689
340.894
350.0207
360.0621
370.196
380.549
390.642
40.946
400.195
410.0171
420.511
430.205
440.0599
450.808
460.259
470.142
480.12
490.0624
50.136
500.462
510.754
520.882
530.97
540.402
550.459
560.313
570.527
580.22
590.457
60.906
600.506
610.567
620.0332
630.314
640.338
650.238
660.75
670.991
680.012
690.754
70.335
700.00114
710.122
720.467
730.206
740.877
750.0274
760.821
770.627
780.307
790.543
80.0218
800.111
810.257
820.389
830.434
840.829
850.0249
860.262
870.043
880.705
890.141
90.769
900.00453
910.486
920.404
930.916
940.239
950.112
960.0542
970.693
980.158
990.945



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: CNhs11218


FANTOM5 (FF) ontology

Direct parent terms


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
0000468 (multi-cellular organism)
0000922 (embryo)
0002113 (kidney)
0000473 (testis)
0002100 (trunk)
0000483 (epithelium)
0000991 (gonad)
0001301 (epididymis)
0001343 (seminiferous tubule of testis)
0000926 (mesoderm)
0000080 (mesonephros)
0000479 (tissue)
0000058 (duct)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0006555 (excretory tube)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0000990 (reproductive system)
0003914 (epithelial tube)
0005103 (mesonephric epithelium)
0000083 (mesonephric tubule)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0003135 (male reproductive organ)
0000119 (cell layer)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0003133 (reproductive organ)
0004175 (internal genitalia)
0005904 (duct of male reproductive system)
0002323 (body cavity)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0003104 (mesenchyme)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0009201 (nephric duct)
0005256 (trunk mesenchyme)
0001048 (primordium)
0003918 (kidney mesenchyme)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0004819 (kidney epithelium)
0004910 (epithelium of male gonad)
0004909 (epithelium of gonad)
0004176 (external genitalia)
0005173 (abdominal segment element)
0005154 (epithelial cord)
0005295 (sex cord)
0002532 (epiblast (generic))
0006553 (renal duct)
0001008 (renal system)
0003101 (male organism)
0003074 (mesonephric duct)
0004122 (genitourinary system)
0000079 (male reproductive system)
0002417 (abdominal segment of trunk)
0006947 (male genital duct)
0000916 (abdomen)
0003887 (intraembryonic coelom)
0002120 (pronephros)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0004054 (internal male genitalia)
0003064 (intermediate mesoderm)
0004875 (nephrogenic cord)
0009196 (indifferent external genitalia)
0009117 (indifferent gonad)
0004871 (somatic layer of lateral plate mesoderm)
0006603 (presumptive mesoderm)
0004876 (urogenital ridge)
0005564 (gonad primordium)
0005297 (testis sex cord)
0004872 (splanchnic layer of lateral plate mesoderm)
0005095 (kidney rudiment)
0005721 (pronephric mesoderm)
0005754 (rostral part of nephrogenic cord)
0003060 (pronephric duct)
0007687 (kidney field)
0005294 (genital ridge)
0010141 (primitive sex cord of indifferent gonad)
0007297 (presumptive pronephric mesoderm)
0005891 (coelomic epithelium)

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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