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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008908
|DRA_sample_Accession=CAGE@SAMD00004714
|accession_numbers=CAGE;DRX009045;DRR009919;DRZ001344;DRZ002727
|accession_numbers=CAGE;DRX009045;DRR009919;DRZ001344;DRZ002727
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001911,UBERON:0000479,UBERON:0004121,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002365,UBERON:0002530,UBERON:0010317,UBERON:0003100,UBERON:0002330
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001911,UBERON:0000479,UBERON:0004121,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002365,UBERON:0002530,UBERON:0010317,UBERON:0003100,UBERON:0002330

Revision as of 21:57, 31 July 2014


Name:mammary gland, adult pregnant day19
Species:Mouse (Mus musculus)
Library ID:CNhs10476
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuemammary gland
dev stage19 days pregnant adult
sexfemale
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  SAMD00004714
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10476 CAGE DRX009045 DRR009919
Accession ID Mm9

Library idBAMCTSS
CNhs10476 DRZ001344 DRZ002727
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

CNhs10476

00
10
100
1000
10000.0687
10010.0331
1002-0.0941
10030.166
10040
10050.106
10060
1007-0.031
10080
10090.121
1010.0476
10100
10110
10120
10130.25
1014-0.0874
1015-0.121
1016-0.0888
10170
10180.106
10190.898
1020
10200
10210.106
10220.326
10230
10240.122
1025-0.0549
10260
1027-0.048
10280
1029-0.0418
1030.0507
10300
1031-0.154
1032-0.119
10330
10340
10350
10360.0507
10370
1038-0.075
10390.121
1040
10400.0463
10411.028



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: CNhs10476

Jaspar motifP-value
MA0002.20.0053
MA0003.10.29
MA0004.10.398
MA0006.10.0943
MA0007.10.199
MA0009.10.259
MA0014.10.427
MA0017.10.659
MA0018.20.0146
MA0019.10.915
MA0024.14.20843e-4
MA0025.10.0425
MA0027.10.979
MA0028.10.829
MA0029.10.0475
MA0030.10.16
MA0031.10.659
MA0035.20.00102
MA0038.10.797
MA0039.20.00515
MA0040.10.0151
MA0041.10.682
MA0042.10.36
MA0043.10.117
MA0046.16.064e-15
MA0047.20.184
MA0048.10.897
MA0050.18.08014e-8
MA0051.12.88699e-5
MA0052.10.922
MA0055.10.459
MA0057.10.244
MA0058.10.429
MA0059.10.349
MA0060.11.75822e-4
MA0061.10.155
MA0062.20.238
MA0065.20.00439
MA0066.10.973
MA0067.10.367
MA0068.10.132
MA0069.10.597
MA0070.10.794
MA0071.10.938
MA0072.10.819
MA0073.10.859
MA0074.10.793
MA0076.10.975
MA0077.10.326
MA0078.10.343
MA0079.20.192
MA0080.23.2988e-5
MA0081.10.0345
MA0083.10.892
MA0084.10.765
MA0087.10.345
MA0088.10.689
MA0090.10.576
MA0091.10.774
MA0092.10.353
MA0093.10.391
MA0099.20.649
MA0100.10.0674
MA0101.10.00964
MA0102.20.11
MA0103.10.00113
MA0104.20.97
MA0105.10.851
MA0106.10.505
MA0107.10.0157
MA0108.20.0108
MA0111.10.501
MA0112.21.16983e-4
MA0113.10.033
MA0114.10.332
MA0115.10.392
MA0116.10.124
MA0117.10.478
MA0119.10.324
MA0122.10.955
MA0124.10.257
MA0125.10.0237
MA0131.10.323
MA0135.10.623
MA0136.19.88118e-4
MA0137.25.08831e-5
MA0138.20.294
MA0139.10.452
MA0140.10.00299
MA0141.10.792
MA0142.10.487
MA0143.10.217
MA0144.11.81966e-5
MA0145.10.0426
MA0146.10.0128
MA0147.10.759
MA0148.10.298
MA0149.10.514
MA0150.10.356
MA0152.10.672
MA0153.13.94373e-11
MA0154.10.0763
MA0155.10.532
MA0156.13.36526e-5
MA0157.10.00542
MA0159.10.221
MA0160.10.832
MA0162.10.329
MA0163.10.141
MA0164.10.28
MA0258.10.0209
MA0259.10.662



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: CNhs10476

Novel motifP-value
10.259
100.284
1000.731
1010.782
1020.635
1030.173
1040.413
1050.318
1060.00183
1070.119
1080.495
1090.0297
110.0956
1100.149
1110.0619
1120.288
1130.815
1140.2
1150.286
1160.311
1170.3
1180.811
1190.139
120.513
1200.814
1210.908
1220.101
1230.629
1240.529
1250.047
1260.715
1270.221
1280.00364
1290.067
134.88599e-6
1300.321
1310.138
1320.632
1330.227
1340.602
1350.106
1360.178
1370.0132
1380.341
1390.148
140.402
1400.864
1410.371
1420.643
1430.388
1440.0778
1450.0392
1460.47
1470.166
1480.705
1490.201
150.224
1500.155
1510.074
1520.0202
1530.425
1540.817
1550.382
1560.691
1570.305
1580.564
1590.778
1600.255
1610.14
1620.293
1630.99
1640.0109
1650.339
1660.765
1670.103
1680.788
1690.0025
170.0412
180.699
190.103
20.299
200.348
210.642
220.0977
230.483
249.01137e-4
250.963
260.0127
270.498
280.418
290.403
30.244
300.775
310.965
320.818
330.614
340.795
350.233
360.724
370.0363
380.146
390.194
40.548
400.446
410.936
420.194
430.0783
440.476
450.65
460.105
470.291
480.0984
490.349
50.168
500.426
510.864
520.0641
530.601
540.853
550.679
560.403
570.958
580.4
590.405
60.184
600.0253
610.129
620.326
630.0187
640.802
650.219
660.776
670.966
680.0999
690.459
70.0594
700.00139
710.128
720.373
730.0169
740.712
750.312
760.707
770.554
780.00541
790.838
80.67
800.792
810.591
820.332
830.806
840.906
850.115
860.189
870.0632
880.364
890.514
90.451
900.639
910.829
920.21
930.693
940.945
950.371
960.484
970.768
980.242
990.324



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: CNhs10476


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)
0001911 (mammary gland)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002365 (exocrine gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0002330 (exocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000317 (mouse pregnant tissue sample)
0000323 (mouse pregnant day 18)
0011387 (mouse mammary gland- adult pregnant day19 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:0006601 (presumptive ectoderm)
UBERON:0008425 (mammary ridge)
UBERON:0010316 (germ layer / neural crest)

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