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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;28
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;28
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;28
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;28
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520adult.CNhs10474.28-22B1.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520adult.CNhs10474.28-22B1.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520adult.CNhs10474.28-22B1.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520adult.CNhs10474.28-22B1.mm10.nobarcode.ctss.bed.gz

Revision as of 18:28, 4 August 2017


Name:lung, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10474
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stageadult
sexmale
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  SAMD00005743
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10474 CAGE DRX009030 DRR009904
Accession ID Mm9

Library idBAMCTSS
CNhs10474 DRZ001329 DRZ002712
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

CNhs10474

00
10
100
1000
10000.0382
10010.171
10020.00476
10030.192
10040
10050.245
10060.0829
1007-0.0748
10080.0736
10090.204
101-0.0767
10100
10110
10120.0736
10130.0666
1014-0.0115
1015-0.191
1016-0.0866
10170
10180.0324
10190
1020
10200
10210
10220.2
10230
10240.47
10251.04
10260
10270
10280.137
10290.206
103-0.0384
10300.24
10310.136
10320.015
10330.0591
10340.284
10350
1036-0.0535
10370.0736
10380.414
10390.0266
1040
10400.519
10410.24



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: CNhs10474

Jaspar motifP-value
MA0002.27.6146e-4
MA0003.10.055
MA0004.10.232
MA0006.10.0677
MA0007.10.994
MA0009.10.553
MA0014.10.452
MA0017.10.0815
MA0018.20.0194
MA0019.10.663
MA0024.18.76242e-5
MA0025.10.00146
MA0027.10.81
MA0028.10.04
MA0029.10.747
MA0030.12.14136e-4
MA0031.13.3352e-6
MA0035.20.235
MA0038.10.748
MA0039.25.93835e-4
MA0040.10.0578
MA0041.10.856
MA0042.10.772
MA0043.10.629
MA0046.11.31541e-5
MA0047.25.89002e-10
MA0048.10.367
MA0050.14.70277e-19
MA0051.11.98694e-10
MA0052.10.439
MA0055.10.574
MA0057.10.351
MA0058.10.141
MA0059.10.00811
MA0060.11.48107e-6
MA0061.10.0334
MA0062.20.685
MA0065.20.531
MA0066.10.335
MA0067.10.829
MA0068.10.416
MA0069.10.675
MA0070.10.985
MA0071.10.198
MA0072.10.179
MA0073.10.843
MA0074.10.35
MA0076.10.0379
MA0077.10.059
MA0078.10.0219
MA0079.20.00811
MA0080.25.2448e-13
MA0081.10.0324
MA0083.10.159
MA0084.10.869
MA0087.10.569
MA0088.10.902
MA0090.10.0749
MA0091.10.289
MA0092.10.908
MA0093.10.229
MA0099.20.472
MA0100.10.408
MA0101.10.0743
MA0102.20.0287
MA0103.10.369
MA0104.20.0132
MA0105.10.821
MA0106.10.0945
MA0107.10.00129
MA0108.20.375
MA0111.10.712
MA0112.20.386
MA0113.10.222
MA0114.10.0228
MA0115.10.193
MA0116.10.537
MA0117.10.685
MA0119.10.0622
MA0122.10.108
MA0124.10.995
MA0125.10.148
MA0131.10.219
MA0135.10.134
MA0136.19.14572e-9
MA0137.20.0902
MA0138.20.855
MA0139.10.0908
MA0140.10.408
MA0141.10.00511
MA0142.10.116
MA0143.10.333
MA0144.10.0137
MA0145.12.07387e-4
MA0146.10.223
MA0147.10.00367
MA0148.11.60559e-8
MA0149.10.956
MA0150.10.986
MA0152.10.681
MA0153.11.6839e-5
MA0154.10.00892
MA0155.10.44
MA0156.15.06007e-11
MA0157.17.11136e-5
MA0159.10.534
MA0160.10.115
MA0162.10.327
MA0163.10.333
MA0164.10.217
MA0258.10.644
MA0259.10.0138



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: CNhs10474

Novel motifP-value
10.903
100.365
1000.215
1010.354
1020.522
1030.337
1040.865
1050.389
1060.00252
1070.0252
1080.896
1090.185
110.9
1100.991
1110.672
1120.484
1130.395
1140.431
1150.732
1160.666
1170.111
1180.683
1190.183
120.75
1200.138
1210.116
1220.631
1230.673
1240.348
1250.478
1260.417
1270.284
1280.00529
1290.139
130.0421
1300.0293
1310.0431
1320.417
1330.662
1340.548
1350.239
1360.498
1370.222
1380.213
1390.987
140.237
1400.5
1410.21
1420.474
1430.603
1440.611
1450.353
1460.492
1470.726
1480.412
1490.0484
150.13
1500.206
1510.0886
1520.0187
1530.721
1540.842
1550.409
1560.0184
1570.656
1580.922
1590.0997
1600.321
1610.712
1620.983
1630.78
1640.953
1650.71
1660.461
1670.143
1680.411
1690.0367
170.51
180.0531
190.105
20.0485
200.247
210.866
220.126
230.0558
240.146
250.358
260.383
270.406
280.47
290.316
30.902
300.483
310.997
320.522
330.714
340.524
350.0934
360.887
370.0784
380.216
390.231
40.978
400.369
410.797
420.799
430.312
440.619
450.0516
460.891
470.577
480.854
490.553
50.747
500.513
510.62
520.0534
530.216
540.71
550.599
560.334
570.365
580.584
590.0661
60.996
600.0352
610.738
620.784
630.291
640.478
650.11
660.309
670.836
680.398
690.783
70.463
700.367
710.803
720.899
730.094
740.804
750.367
760.437
770.285
780.729
790.972
80.706
800.201
810.639
820.591
830.095
840.472
850.189
860.856
870.93
880.832
890.435
90.199
900.509
910.598
920.362
930.0724
940.306
950.654
960.439
970.626
980.401
990.408



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: CNhs10474


FANTOM5 (FF) ontology

Direct parent terms

part_of relathionship
UBERON:0000310 breast

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)
0002048 (lung)
0000310 (breast)
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)
0001443 (chest)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011307 (mouse lung- adult 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)

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