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{{f5samples
{{f5samples
|id=FF:595-22B6
|id=FF:595-22B6
|name=mammary gland, adult lactating day02, biol_rep1
|name=mammary gland, adult lactating day02
|sample_id=595
|sample_id=595
|rna_tube_id=595-22B6
|rna_tube_id=22B6
|rna_box=595-22B6
|rna_box=22
|rna_position=595-22B6
|rna_position=B6
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
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|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs10480,LSID647,,COMPLETED
|profile_hcage=CNhs10480,LSID647,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:42, 27 February 2012


Name:mammary gland, adult lactating day02
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuemammary gland
dev stage2 days lactation 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
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

CNhs10480

00
10
100
1000
10000.2
10010.0326
1002-0.0577
10030.16
10040
10050
10060
1007-0.00387
10080
10090.0377
1011.64964e-4
10100
1011-3.231029e-4
10120
10130.555
1014-0.0874
1015-0.221
1016-0.206
10170
10180.181
10191.954
1020
10200
10210.0648
10220.394
10230
10240.0865
10250
10260
10270
10280
1029-0.0455
1030
10300
1031-0.424
10320.0723
10330
10340
10350
1036-0.0646
10370
1038-0.14
10390.122
1040
1040-0.121
10411.015



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: CNhs10480

Jaspar motifP-value
MA0002.20.00288
MA0003.10.293
MA0004.10.751
MA0006.10.127
MA0007.10.274
MA0009.10.433
MA0014.10.393
MA0017.10.219
MA0018.20.0268
MA0019.10.822
MA0024.10.0162
MA0025.10.3
MA0027.10.406
MA0028.10.758
MA0029.10.243
MA0030.10.0433
MA0031.10.711
MA0035.20.0137
MA0038.10.58
MA0039.20.00679
MA0040.10.0183
MA0041.10.225
MA0042.10.132
MA0043.10.0897
MA0046.11.22044e-12
MA0047.20.807
MA0048.10.952
MA0050.16.18869e-4
MA0051.13.86315e-4
MA0052.10.634
MA0055.10.505
MA0057.10.158
MA0058.10.591
MA0059.10.23
MA0060.10.204
MA0061.10.264
MA0062.20.488
MA0065.20.00183
MA0066.10.588
MA0067.10.654
MA0068.10.705
MA0069.10.379
MA0070.10.465
MA0071.10.961
MA0072.10.667
MA0073.10.79
MA0074.10.646
MA0076.10.741
MA0077.10.241
MA0078.10.489
MA0079.20.972
MA0080.29.24739e-4
MA0081.10.123
MA0083.10.814
MA0084.10.71
MA0087.10.399
MA0088.10.396
MA0090.10.985
MA0091.10.382
MA0092.10.261
MA0093.10.659
MA0099.20.319
MA0100.10.215
MA0101.10.205
MA0102.20.321
MA0103.11.51835e-4
MA0104.20.951
MA0105.10.376
MA0106.10.296
MA0107.10.119
MA0108.20.0942
MA0111.10.614
MA0112.21.14672e-4
MA0113.10.0406
MA0114.10.104
MA0115.10.548
MA0116.10.0993
MA0117.10.341
MA0119.10.143
MA0122.10.9
MA0124.10.226
MA0125.10.0989
MA0131.10.459
MA0135.10.833
MA0136.10.0145
MA0137.28.6792e-5
MA0138.20.578
MA0139.10.372
MA0140.10.0349
MA0141.10.521
MA0142.10.487
MA0143.10.212
MA0144.11.20247e-4
MA0145.10.0563
MA0146.10.0101
MA0147.10.692
MA0148.10.691
MA0149.10.186
MA0150.10.0863
MA0152.10.218
MA0153.16.99199e-7
MA0154.10.0509
MA0155.10.596
MA0156.10.0184
MA0157.10.152
MA0159.10.0385
MA0160.10.538
MA0162.10.248
MA0163.10.0489
MA0164.10.273
MA0258.10.0149
MA0259.10.688



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: CNhs10480

Novel motifP-value
10.202
100.0878
1000.791
1010.915
1020.434
1030.0713
1040.739
1050.374
1060.0163
1070.199
1080.385
1090.0188
110.0507
1100.0978
1110.0235
1120.166
1130.976
1140.36
1150.14
1160.405
1170.126
1180.976
1190.0348
120.451
1200.665
1210.638
1220.0874
1230.441
1240.666
1250.0566
1260.641
1270.253
1280.0114
1290.137
132.7623e-5
1300.839
1310.142
1320.752
1330.362
1340.38
1350.119
1360.685
1370.0959
1380.652
1390.0759
140.617
1400.593
1410.222
1420.406
1430.696
1440.0532
1450.0302
1460.285
1470.331
1480.461
1490.148
150.182
1500.151
1510.141
1520.0303
1530.469
1540.865
1550.814
1560.349
1570.388
1580.302
1590.557
1600.283
1610.52
1620.525
1630.403
1640.153
1650.23
1660.791
1670.414
1680.735
1690.00115
170.0251
180.915
190.105
20.425
200.435
210.792
220.139
230.33
240.0169
250.539
260.0321
270.597
280.477
290.221
30.17
300.871
310.736
320.714
330.366
340.93
350.815
360.303
370.041
380.15
390.178
40.955
400.466
410.954
420.184
430.183
440.228
450.759
460.126
470.0886
480.128
490.214
50.133
500.633
510.65
520.184
530.993
540.869
550.352
560.331
570.415
580.242
590.429
60.345
600.0585
610.167
620.135
630.0252
640.612
650.189
660.927
670.933
680.025
690.626
70.0458
700.00253
710.0487
720.304
730.0253
740.981
750.187
760.735
770.282
780.0143
790.937
80.283
800.616
810.41
820.569
830.84
840.794
850.0616
860.205
870.153
880.219
890.15
90.846
900.904
910.317
920.198
930.835
940.958
950.272
960.827
970.915
980.145
990.351



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: CNhs10480


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)
0000076 (external ectoderm)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001048 (primordium)
0001062 (anatomical entity)
0001911 (mammary gland)
0002050 (embryonic structure)
0002330 (exocrine system)
0002365 (exocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0003100 (female organism)
0004121 (ectoderm-derived structure)
0005085 (ectodermal placode)
0005153 (epithelial bud)
0005291 (embryonic tissue)
0005311 (mammary placode)
0005333 (mammary bud)
0005423 (developing anatomical structure)
0007023 (adult organism)
0008425 (mammary ridge)

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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