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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008905
|DRA_sample_Accession=CAGE@SAMD00005110
|accession_numbers=CAGE;DRX009042;DRR009916;DRZ001341;DRZ002724
|accession_numbers=CAGE;DRX009042;DRR009916;DRZ001341;DRZ002724
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915

Revision as of 21:37, 31 July 2014


Name:lung, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11119
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stage25 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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005110
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11119 CAGE DRX009042 DRR009916
Accession ID Mm9

Library idBAMCTSS
CNhs11119 DRZ001341 DRZ002724
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

CNhs11119

00
10
100.061
1000
10000.125
10010.239
1002-0.0136
10030.127
10040
10050.171
10060.202
10070.0478
10080
10090.365
101-0.0861
10100
1011-0.0314
10120.181
10130.0727
10140.129
1015-0.182
10160.0533
10170
10180
10190
1020
10200
10210
10220.156
10230
10240.589
10251.121
10260
10270
10280.0692
10290.473
1030.175
10300.407
10310.287
10320.0642
10330
10340.228
10350.0692
1036-0.157
10370.019
10380.508
10390.0897
1040
10400.491
10410.344



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: CNhs11119

Jaspar motifP-value
MA0002.20.294
MA0003.10.0946
MA0004.10.0747
MA0006.10.0458
MA0007.10.311
MA0009.10.364
MA0014.10.688
MA0017.10.202
MA0018.21.48844e-5
MA0019.10.898
MA0024.17.6534e-4
MA0025.10.791
MA0027.10.665
MA0028.10.0117
MA0029.10.72
MA0030.10.376
MA0031.10.0677
MA0035.20.0876
MA0038.10.668
MA0039.20.00326
MA0040.10.56
MA0041.10.257
MA0042.10.503
MA0043.10.00212
MA0046.11.63639e-9
MA0047.26.40277e-5
MA0048.10.857
MA0050.17.01164e-8
MA0051.11.9027e-4
MA0052.10.0615
MA0055.10.818
MA0057.10.277
MA0058.10.05
MA0059.10.0874
MA0060.18.97089e-10
MA0061.10.0223
MA0062.20.0152
MA0065.20.863
MA0066.10.876
MA0067.10.683
MA0068.10.939
MA0069.10.655
MA0070.10.532
MA0071.10.285
MA0072.10.341
MA0073.10.801
MA0074.10.566
MA0076.10.00459
MA0077.10.0116
MA0078.10.00438
MA0079.20.0609
MA0080.27.75867e-10
MA0081.10.194
MA0083.10.0337
MA0084.10.816
MA0087.10.562
MA0088.10.725
MA0090.10.0891
MA0091.10.623
MA0092.10.484
MA0093.10.0695
MA0099.20.273
MA0100.10.137
MA0101.10.143
MA0102.20.366
MA0103.10.93
MA0104.20.00285
MA0105.10.178
MA0106.10.0223
MA0107.10.00522
MA0108.20.433
MA0111.10.438
MA0112.20.0134
MA0113.10.87
MA0114.10.0345
MA0115.10.0971
MA0116.10.14
MA0117.10.378
MA0119.10.0369
MA0122.10.242
MA0124.10.52
MA0125.10.0519
MA0131.10.22
MA0135.10.263
MA0136.10.0068
MA0137.20.917
MA0138.20.828
MA0139.10.0648
MA0140.10.824
MA0141.10.0694
MA0142.10.869
MA0143.10.287
MA0144.10.345
MA0145.10.00151
MA0146.10.323
MA0147.10.00168
MA0148.11.71498e-4
MA0149.10.65
MA0150.10.37
MA0152.10.213
MA0153.13.11583e-7
MA0154.10.00366
MA0155.10.158
MA0156.10.0013
MA0157.10.0645
MA0159.10.83
MA0160.10.0888
MA0162.10.16
MA0163.10.74
MA0164.10.401
MA0258.10.242
MA0259.10.0108



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: CNhs11119

Novel motifP-value
10.641
100.815
1000.26
1010.496
1020.588
1030.282
1040.619
1050.439
1069.21095e-4
1070.00577
1080.667
1090.172
110.859
1100.867
1110.867
1120.201
1130.975
1140.386
1150.535
1160.914
1170.326
1180.812
1190.0804
120.681
1200.169
1210.638
1220.815
1230.96
1240.579
1250.449
1260.292
1270.223
1280.00447
1290.0879
130.0147
1300.00761
1310.126
1320.338
1330.463
1340.744
1350.583
1360.337
1370.326
1380.0496
1390.643
140.29
1400.561
1410.265
1420.315
1430.611
1440.721
1450.168
1460.819
1470.825
1480.306
1490.125
150.414
1500.145
1510.181
1520.0251
1530.583
1540.321
1550.678
1560.357
1570.975
1580.915
1590.0333
1600.0752
1610.466
1620.403
1630.852
1640.568
1650.766
1660.235
1670.764
1680.945
1690.00869
170.345
180.155
190.036
20.129
200.374
210.617
220.103
230.0333
240.316
250.324
260.0626
270.867
280.52
290.511
30.454
300.86
310.884
320.714
330.74
340.421
350.315
360.871
370.0403
380.199
390.076
40.715
400.61
410.392
420.607
430.135
440.577
450.169
460.687
470.629
480.894
490.261
50.521
500.321
510.659
520.0668
530.402
540.806
550.895
560.356
570.998
580.586
590.0478
60.923
600.0336
610.739
620.803
630.142
640.716
650.201
660.105
670.491
680.632
690.986
70.346
700.437
710.308
720.91
730.145
740.475
750.751
760.718
770.23
780.861
790.616
80.883
800.811
810.858
820.329
830.253
840.279
850.0422
860.826
870.0206
880.979
890.343
90.154
900.642
910.167
920.136
930.595
940.864
950.656
960.813
970.847
980.704
990.259



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: CNhs11119


FANTOM5 (FF) ontology

Direct parent terms

part_of relathionship
UBERON:0000170 pair of lungs

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)
0002048 (lung)
0002100 (trunk)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000309 (mouse neonate N25 sample)
0011488 (mouse lung- neonate N25 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:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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