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|profile_rnaseq=,,,
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|repeat_enrich_byfamily=0.309621626674781,0,0,0,0,0.117946305307076,0.327498749012386,0,0.0082716889057459,0,0,0.202591464974938,0,0,0,0,0,0,0.0187128228479983,0,0,0,0.351825418422672,0,0,0,0,0,0,0,0,0,0.443704052396548,0,0,0,0.799660323566278,0,-0.03341001628449,-0.0642983270704141,-0.0233371678777377,0.460383601989688,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,0.22092515780804,0,0,0,0,-0.0237583952881394,0,0.0717419398884913,0,0,0,0.192527445792385,-0.0237199519679062,0.0525151309594904,0.0983435310688386,0,0.032918362238592,-0.0149871250073208,0,0,0,0,-0.228850584369725,0.348614269677482,0.0391147104671686,0,0,0,0,0,0,0.212971178032784,0.356494034113171,0.0171277031400809,0,0,0,0,0
|rna_box=24
|rna_box=24
|rna_catalog_number=
|rna_catalog_number=

Revision as of 10:46, 24 September 2012


Name:liver, neonate N10
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage10 days neonate
sexmixture
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

CNhs11115

00
10
100
1000
10000.0235
10010.148
1002-0.0388
1003-0.00256
10040
10050.0791
10060.021
1007-0.0614
10080
10090.0272
101-0.0232
10100
1011-0.168
10120
10130.39
10140.00534
1015-0.166
10160.0251
10170
10180
10190
1020
10200
10210
10220.193
10230
10240
10250.617
10260
10270
10280
10290.0278
1030
10300.118
1031-0.0163
1032-0.177
10330
10340.647
10350
10360.0301
10370
1038-0.0566
10390.487
1040
1040-0.152
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



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: CNhs11115

Jaspar motifP-value
MA0002.20.134
MA0003.10.364
MA0004.10.942
MA0006.10.197
MA0007.10.489
MA0009.10.552
MA0014.10.55
MA0017.13.28214e-20
MA0018.28.29836e-7
MA0019.10.505
MA0024.10.145
MA0025.10.319
MA0027.10.421
MA0028.10.935
MA0029.10.35
MA0030.10.03
MA0031.10.049
MA0035.20.314
MA0038.10.736
MA0039.20.704
MA0040.10.496
MA0041.10.195
MA0042.10.539
MA0043.10.0337
MA0046.14.63389e-77
MA0047.24.37195e-7
MA0048.10.297
MA0050.10.00242
MA0051.10.00973
MA0052.10.0805
MA0055.10.346
MA0057.10.842
MA0058.10.811
MA0059.10.286
MA0060.10.00381
MA0061.10.332
MA0062.20.735
MA0065.24.75763e-14
MA0066.10.0133
MA0067.10.027
MA0068.10.247
MA0069.10.271
MA0070.10.296
MA0071.16.03811e-4
MA0072.11.29276e-4
MA0073.10.575
MA0074.10.308
MA0076.10.553
MA0077.10.0179
MA0078.10.531
MA0079.20.321
MA0080.20.181
MA0081.10.837
MA0083.10.271
MA0084.10.434
MA0087.10.233
MA0088.10.579
MA0090.10.503
MA0091.10.884
MA0092.10.0518
MA0093.10.932
MA0099.20.198
MA0100.10.274
MA0101.10.784
MA0102.20.326
MA0103.10.31
MA0104.20.559
MA0105.10.0321
MA0106.10.0517
MA0107.10.98
MA0108.20.051
MA0111.10.86
MA0112.21.37527e-6
MA0113.10.531
MA0114.12.4388e-20
MA0115.14.61353e-10
MA0116.10.0841
MA0117.10.918
MA0119.10.00558
MA0122.10.401
MA0124.10.505
MA0125.10.882
MA0131.10.921
MA0135.10.57
MA0136.10.88
MA0137.20.331
MA0138.20.381
MA0139.10.0692
MA0140.10.336
MA0141.11.67293e-5
MA0142.10.211
MA0143.10.127
MA0144.10.549
MA0145.10.13
MA0146.10.201
MA0147.10.674
MA0148.19.56357e-11
MA0149.10.049
MA0150.10.0849
MA0152.10.271
MA0153.13.21055e-51
MA0154.10.0592
MA0155.10.374
MA0156.10.911
MA0157.10.0211
MA0159.12.43601e-4
MA0160.10.00134
MA0162.10.493
MA0163.13.50784e-5
MA0164.10.956
MA0258.10.00436
MA0259.10.368



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: CNhs11115

Novel motifP-value
10.128
100.143
1000.66
1010.986
1020.0928
1030.0156
1040.555
1050.827
1060.0403
1070.0387
1080.383
1090.0684
110.113
1100.0424
1110.0782
1120.00567
1130.899
1140.0371
1150.861
1160.905
1170.0793
1180.188
1190.0979
120.593
1200.562
1210.767
1220.606
1230.289
1240.409
1250.277
1260.336
1270.55
1280.0286
1290.638
138.1832e-5
1300.617
1310.157
1320.494
1330.503
1340.816
1350.476
1360.387
1370.976
1380.217
1390.852
140.409
1400.0187
1410.383
1420.363
1430.843
1440.749
1450.0481
1460.383
1470.449
1480.592
1490.712
150.177
1500.227
1510.551
1520.142
1530.115
1540.479
1550.988
1560.271
1570.298
1580.343
1590.701
1600.147
1610.868
1620.523
1630.828
1640.17
1650.34
1660.235
1670.226
1680.571
1698.91765e-4
170.0707
180.899
190.014
20.751
200.493
210.477
220.131
230.327
240.254
250.745
262.42e-4
270.725
280.452
290.391
30.0436
300.911
310.4
320.19
330.298
340.864
350.887
360.0755
370.0618
380.269
390.287
40.803
400.197
410.505
420.276
430.0577
440.249
450.659
460.092
470.384
480.21
490.0589
50.124
500.531
510.319
520.291
530.726
540.336
550.583
560.435
570.742
580.315
590.214
60.979
600.134
610.193
620.172
630.125
640.593
650.233
660.802
670.87
680.208
690.684
70.142
700.164
710.0408
720.753
730.148
740.762
750.055
760.995
770.46
780.0203
790.797
80.0119
800.637
810.607
820.0553
830.974
840.961
850.0589
860.144
870.569
880.663
890.0304
90.5
900.15
910.222
920.194
930.28
940.934
950.396
960.163
970.812
980.361
990.0558



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: CNhs11115


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)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011416 (mouse liver- neonate N10 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:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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