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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005687
|DRA_sample_Accession=CAGE@SAMD00005687
|accession_numbers=CAGE;DRX008953;DRR009827;DRZ001252;DRZ002635
|accession_numbers=CAGE;DRX008953;DRR009827;DRZ001252;DRZ002635;DRZ012602;DRZ013985
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001301,UBERON:0000479,UBERON:0000058,UBERON:0005156,UBERON:0000062,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0005904,UBERON:0004175,UBERON:0010317,UBERON:0003101,UBERON:0000079,UBERON:0006947,UBERON:0004054
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001301,UBERON:0000479,UBERON:0000058,UBERON:0005156,UBERON:0000062,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0005904,UBERON:0004175,UBERON:0010317,UBERON:0003101,UBERON:0000079,UBERON:0006947,UBERON:0004054
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:40, 10 August 2017


Name:epididymis, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10490
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueepididymis
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005687
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10490 CAGE DRX008953 DRR009827
Accession ID Mm9

Library idBAMCTSS
CNhs10490 DRZ001252 DRZ002635
Accession ID Mm10

Library idBAMCTSS
CNhs10490 DRZ012602 DRZ013985
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs10490

00
10
100
1000
10000
10010.0774
10020.0663
1003-0.00448
10040
1005-0.0389
1006-0.143
1007-0.0817
10080
10090.211
101-0.0713
10100
10110.157
10120
10130.526
1014-0.0874
1015-0.125
1016-0.278
10170
10180.389
10190.0979
1020
10200
10210
10220.355
10230
1024-0.0454
10250
10261.228
1027-0.048
10280
1029-0.0498
103-0.0708
10300
1031-0.151
10320.178
10330
10340.245
10350
10360.116
10370.0979
10380.00513
10390.00779
1040
1040-0.184
10410.303



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



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: CNhs10490

Jaspar motifP-value
MA0002.20.00383
MA0003.10.0196
MA0004.10.649
MA0006.10.469
MA0007.17.7873e-12
MA0009.10.137
MA0014.10.00481
MA0017.10.597
MA0018.20.619
MA0019.10.489
MA0024.11.14036e-5
MA0025.10.203
MA0027.10.72
MA0028.10.0277
MA0029.10.0557
MA0030.10.478
MA0031.10.378
MA0035.20.007
MA0038.10.32
MA0039.20.0147
MA0040.10.0695
MA0041.10.452
MA0042.10.441
MA0043.10.0102
MA0046.10.001
MA0047.20.752
MA0048.10.289
MA0050.10.039
MA0051.10.0353
MA0052.10.002
MA0055.10.0128
MA0057.10.186
MA0058.10.221
MA0059.10.304
MA0060.10.349
MA0061.10.371
MA0062.20.00623
MA0065.20.329
MA0066.10.549
MA0067.10.62
MA0068.10.027
MA0069.10.0135
MA0070.10.648
MA0071.10.361
MA0072.10.374
MA0073.10.63
MA0074.10.991
MA0076.10.0291
MA0077.10.425
MA0078.10.726
MA0079.20.427
MA0080.20.111
MA0081.10.349
MA0083.10.45
MA0084.10.789
MA0087.10.346
MA0088.10.0753
MA0090.10.803
MA0091.10.418
MA0092.10.991
MA0093.10.67
MA0099.20.591
MA0100.10.426
MA0101.10.147
MA0102.20.0404
MA0103.17.21146e-7
MA0104.20.71
MA0105.10.42
MA0106.10.538
MA0107.10.111
MA0108.23.15706e-7
MA0111.10.818
MA0112.20.00143
MA0113.15.52886e-7
MA0114.10.634
MA0115.10.57
MA0116.10.376
MA0117.10.532
MA0119.10.277
MA0122.10.927
MA0124.10.184
MA0125.10.133
MA0131.10.8
MA0135.10.772
MA0136.10.0296
MA0137.20.353
MA0138.20.872
MA0139.10.249
MA0140.10.00279
MA0141.10.774
MA0142.10.926
MA0143.10.684
MA0144.10.153
MA0145.10.176
MA0146.10.0111
MA0147.10.875
MA0148.10.397
MA0149.10.0482
MA0150.10.821
MA0152.10.557
MA0153.10.0117
MA0154.10.453
MA0155.10.391
MA0156.10.0452
MA0157.10.974
MA0159.10.0809
MA0160.10.421
MA0162.10.256
MA0163.10.0426
MA0164.10.874
MA0258.10.035
MA0259.10.848



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: CNhs10490

Novel motifP-value
10.299
100.169
1000.287
1010.56
1020.103
1030.0318
1040.116
1050.684
1060.281
1070.734
1080.353
1090.0322
110.242
1100.693
1110.00242
1120.00627
1130.0636
1140.0781
1150.737
1160.897
1170.198
1180.512
1190.0205
120.918
1200.518
1210.436
1220.0973
1230.485
1240.136
1250.4
1260.137
1270.948
1280.256
1290.0926
133.86869e-5
1300.335
1310.909
1320.607
1330.618
1340.998
1350.789
1360.121
1370.805
1380.262
1390.0414
140.602
1400.28
1410.8
1420.862
1430.317
1440.201
1450.235
1460.35
1470.892
1480.508
1492.99086e-5
157.3164e-4
1500.598
1510.4
1520.0734
1530.406
1540.705
1550.759
1560.326
1570.493
1580.214
1590.263
1600.31
1610.305
1620.99
1630.032
1640.0131
1650.00514
1660.376
1670.945
1680.637
1690.00199
170.182
180.504
190.0777
20.607
200.479
210.0694
220.185
230.436
240.0194
250.673
260.0144
270.476
280.613
290.0246
30.29
300.801
310.732
320.915
330.664
340.472
350.848
360.261
370.0247
380.258
390.085
40.676
400.111
410.713
420.973
430.21
440.0209
450.328
460.157
470.0907
480.0911
490.105
50.287
500.766
510.708
520.833
530.674
540.732
550.0735
560.803
570.679
580.0866
590.751
60.0844
600.155
610.429
620.0641
630.166
640.532
650.678
660.633
670.719
680.978
690.031
70.128
700.0049
710.222
720.512
730.0407
740.429
750.138
760.612
770.568
780.933
790.599
80.315
800.239
810.691
820.0404
830.424
840.946
850.123
860.233
870.0319
880.727
890.291
90.95
900.869
910.181
920.216
930.261
940.602
950.172
960.134
970.296
980.237
990.296



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: CNhs10490


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)
0007023 (adult organism)
0001301 (epididymis)
0000479 (tissue)
0000058 (duct)
0005156 (reproductive structure)
0000062 (organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0005904 (duct of male reproductive system)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)
0006947 (male genital duct)
0004054 (internal male genitalia)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011289 (epididymis- adult sample)

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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0007297 (presumptive pronephric mesoderm)
UBERON:0010316 (germ layer / neural crest)

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