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FF:750-23E6

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Name:lung, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11219
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuelung
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005871
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11219 CAGE DRX009040 DRR009914
Accession ID Mm9

Library idBAMCTSS
CNhs11219 DRZ001339 DRZ002722
Accession ID Mm10

Library idBAMCTSS
CNhs11219 DRZ012689 DRZ014072
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

CNhs11219

00
10
100
1000
10000.0643
10010.165
1002-0.0845
10030.184
10040
10050.0813
10060.149
10070.103
10080
10090.415
101-0.0689
10100
1011-0.0835
10120.0643
10130.0055
10140.0847
10150.058
10160.352
10170
10180
10190
1020
10200
10210.0156
10220.0109
10230
10240.562
10251.22
10260
10270.00328
10280
10290.455
1030.228
10300.255
10310.533
10320.0856
1033-0.0752
10340.12
10350.0643
1036-0.194
10370
10380.698
1039-0.0641
1040
10400.522
10410.255



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: CNhs11219

Jaspar motifP-value
MA0002.20.389
MA0003.10.288
MA0004.10.023
MA0006.10.0373
MA0007.10.172
MA0009.10.783
MA0014.10.929
MA0017.14.84668e-5
MA0018.20.00577
MA0019.10.756
MA0024.10.206
MA0025.10.573
MA0027.10.45
MA0028.10.00137
MA0029.10.607
MA0030.10.0118
MA0031.10.0282
MA0035.20.00777
MA0038.10.778
MA0039.20.0554
MA0040.10.562
MA0041.10.349
MA0042.10.738
MA0043.10.224
MA0046.12.71266e-8
MA0047.24.82481e-6
MA0048.10.828
MA0050.10.0219
MA0051.10.0551
MA0052.10.238
MA0055.10.845
MA0057.10.678
MA0058.10.0039
MA0059.17.61001e-5
MA0060.10.00121
MA0061.10.696
MA0062.26.57742e-4
MA0065.20.00159
MA0066.10.196
MA0067.10.613
MA0068.10.591
MA0069.10.955
MA0070.10.978
MA0071.10.00609
MA0072.10.0427
MA0073.10.627
MA0074.10.715
MA0076.15.35948e-4
MA0077.10.418
MA0078.10.0109
MA0079.20.0408
MA0080.20.00542
MA0081.10.275
MA0083.14.07066e-6
MA0084.10.887
MA0087.10.753
MA0088.10.102
MA0090.10.0137
MA0091.10.304
MA0092.10.896
MA0093.10.0191
MA0099.20.0451
MA0100.10.162
MA0101.10.38
MA0102.20.677
MA0103.10.0187
MA0104.21.45973e-4
MA0105.10.037
MA0106.10.147
MA0107.10.0116
MA0108.20.966
MA0111.10.778
MA0112.20.0399
MA0113.10.445
MA0114.11.38439e-6
MA0115.10.00334
MA0116.10.00963
MA0117.10.206
MA0119.10.449
MA0122.10.285
MA0124.10.122
MA0125.10.185
MA0131.10.281
MA0135.10.579
MA0136.10.886
MA0137.20.312
MA0138.20.372
MA0139.10.608
MA0140.10.146
MA0141.12.87719e-6
MA0142.10.395
MA0143.10.841
MA0144.10.882
MA0145.10.0098
MA0146.10.795
MA0147.11.22156e-5
MA0148.11.95608e-4
MA0149.10.638
MA0150.18.42972e-4
MA0152.10.274
MA0153.11.62036e-6
MA0154.10.681
MA0155.10.507
MA0156.10.161
MA0157.10.101
MA0159.10.00172
MA0160.11.55929e-4
MA0162.10.764
MA0163.19.27748e-4
MA0164.10.504
MA0258.10.0132
MA0259.10.019



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: CNhs11219

Novel motifP-value
10.176
100.0512
1000.187
1010.721
1020.839
1030.295
1040.774
1050.416
1060.0846
1070.00872
1080.638
1090.3
110.107
1100.125
1110.0628
1120.882
1130.875
1140.161
1150.369
1160.275
1170.0125
1180.302
1190.965
120.496
1200.131
1210.168
1220.596
1230.991
1240.586
1250.672
1260.691
1270.196
1280.0563
1290.812
130.891
1300.0344
1310.0886
1320.438
1330.366
1340.777
1350.359
1360.871
1370.44
1380.0957
1390.237
140.732
1400.998
1410.749
1420.82
1430.457
1440.792
1450.923
1460.942
1470.389
1480.82
1490.371
150.376
1500.326
1510.728
1520.0389
1530.542
1540.685
1550.664
1560.4
1570.713
1580.879
1590.0413
1600.498
1610.713
1620.287
1630.714
1640.493
1650.19
1660.0782
1670.521
1680.748
1690.462
170.483
180.00632
190.295
20.33
200.378
210.915
220.495
230.221
240.761
250.0479
260.507
270.543
280.836
290.0364
30.223
300.565
310.466
320.299
330.448
340.462
350.0107
360.186
370.739
380.629
390.174
40.782
400.777
410.292
420.534
430.995
440.0303
450.253
460.314
470.245
480.176
490.416
50.71
500.341
510.828
520.0886
530.582
540.948
550.666
560.884
570.175
580.646
590.62
60.636
600.246
610.743
620.195
630.91
640.12
650.958
660.166
670.865
680.33
690.21
70.687
700.0679
710.0641
720.441
730.989
740.915
750.0271
760.613
770.425
780.192
790.982
80.0496
800.451
810.0567
820.414
830.854
840.862
850.952
860.692
870.0043
880.728
890.378
90.424
900.00693
910.576
920.827
930.577
940.269
950.45
960.106
970.581
980.272
990.595



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: CNhs11219


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)
0000305 (mouse neonate N10 sample)
0011415 (mouse lung- 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: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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