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|library_id=CNhs10583
|library_id=CNhs10583
|library_id_phase_based=2:CNhs10583
|library_id_phase_based=2:CNhs10583
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;1287
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1287
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E18.CNhs10583.1287-20I6.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E18.CNhs10583.1287-20I6.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E18.CNhs10583.1287-20I6.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520embryo%2520E18.CNhs10583.1287-20I6.mm10.nobarcode.ctss.bed.gz

Revision as of 22:05, 18 May 2017


Name:lung, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs10583
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stage18 days embryo
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  SAMD00005648
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10583 CAGE DRX009036 DRR009910
Accession ID Mm9

Library idBAMCTSS
CNhs10583 DRZ001335 DRZ002718
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

CNhs10583

00
10
100
1000
10000.0454
10010.0496
1002-0.0137
10030.0821
10040
10050.0927
10060
10070.0808
10080
10090.307
101-0.0911
10100
1011-0.0539
10120
10130.0161
10140.0927
1015-0.0607
10160.148
10170
10180.171
10190
1020
10200.0927
1021-0.0487
10220.0726
10230
10240.542
10251.051
10260
10270
10280
10290.0864
1030.0966
10300
10310.437
1032-0.0838
10330
10340.299
10350
1036-0.183
10370
10380.427
1039-0.0359
1040
10400.397
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: CNhs10583

Jaspar motifP-value
MA0002.20.0905
MA0003.10.0712
MA0004.10.0199
MA0006.10.0497
MA0007.10.31
MA0009.10.953
MA0014.10.736
MA0017.18.57076e-4
MA0018.20.00816
MA0019.10.583
MA0024.10.122
MA0025.10.209
MA0027.10.802
MA0028.10.0618
MA0029.10.808
MA0030.10.00228
MA0031.10.00284
MA0035.20.0647
MA0038.10.187
MA0039.20.00408
MA0040.10.442
MA0041.10.945
MA0042.10.78
MA0043.10.912
MA0046.10.458
MA0047.22.05155e-10
MA0048.10.653
MA0050.10.0531
MA0051.10.0475
MA0052.10.0213
MA0055.10.215
MA0057.10.575
MA0058.10.00511
MA0059.13.38948e-5
MA0060.10.7
MA0061.10.761
MA0062.20.0196
MA0065.20.0397
MA0066.10.0266
MA0067.10.329
MA0068.10.279
MA0069.10.317
MA0070.10.318
MA0071.10.0089
MA0072.10.201
MA0073.10.822
MA0074.10.433
MA0076.10.0651
MA0077.10.437
MA0078.10.0256
MA0079.20.0108
MA0080.20.105
MA0081.10.729
MA0083.13.18959e-4
MA0084.10.684
MA0087.10.278
MA0088.10.45
MA0090.10.00452
MA0091.10.151
MA0092.10.85
MA0093.10.0281
MA0099.20.0706
MA0100.10.972
MA0101.10.789
MA0102.20.191
MA0103.10.372
MA0104.22.1977e-4
MA0105.10.27
MA0106.10.316
MA0107.10.147
MA0108.20.031
MA0111.10.989
MA0112.20.195
MA0113.10.623
MA0114.12.53942e-4
MA0115.10.0152
MA0116.10.299
MA0117.10.0724
MA0119.10.1
MA0122.10.0935
MA0124.10.302
MA0125.10.728
MA0131.10.335
MA0135.10.12
MA0136.10.896
MA0137.20.93
MA0138.20.277
MA0139.10.473
MA0140.10.668
MA0141.15.19195e-7
MA0142.10.349
MA0143.10.952
MA0144.10.614
MA0145.10.00244
MA0146.10.309
MA0147.11.90183e-5
MA0148.17.79001e-9
MA0149.10.555
MA0150.10.00223
MA0152.10.907
MA0153.10.853
MA0154.10.279
MA0155.10.089
MA0156.10.237
MA0157.10.0344
MA0159.10.0183
MA0160.10.00573
MA0162.10.407
MA0163.10.105
MA0164.10.388
MA0258.10.0171
MA0259.10.0933



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: CNhs10583

Novel motifP-value
10.115
100.108
1000.408
1010.671
1020.914
1030.633
1040.886
1050.706
1060.131
1070.0757
1080.998
1090.989
110.211
1100.713
1110.169
1120.442
1130.731
1140.429
1150.513
1160.826
1170.0155
1180.406
1190.51
120.379
1200.07
1210.337
1220.999
1230.747
1240.582
1250.528
1260.847
1270.585
1280.266
1290.819
130.0198
1300.0199
1310.0286
1320.48
1330.775
1340.399
1350.849
1360.0309
1370.84
1380.243
1390.187
140.759
1400.141
1410.454
1420.752
1430.185
1440.904
1450.746
1460.966
1470.554
1480.225
1490.131
150.344
1500.165
1510.465
1520.0133
1530.486
1540.471
1550.962
1560.00831
1570.655
1580.655
1590.187
1600.233
1610.647
1620.428
1630.715
1640.93
1650.697
1660.346
1670.0106
1680.988
1690.143
170.645
180.00152
190.243
20.0918
200.358
210.931
220.216
230.366
240.374
250.0975
260.385
270.895
280.981
290.25
30.549
300.374
310.325
320.085
330.72
340.635
350.0024
360.372
370.552
380.685
390.25
40.484
400.702
410.409
420.686
430.901
440.0291
450.107
460.276
470.261
480.22
490.151
50.746
500.228
510.798
520.121
530.632
540.804
550.688
560.966
570.261
580.786
590.202
60.748
600.253
610.654
620.294
630.732
640.232
650.876
660.317
670.949
680.225
690.361
70.772
700.0552
710.441
720.272
730.343
740.993
750.146
760.413
770.341
780.221
790.977
80.125
800.503
810.0573
820.763
830.262
840.712
850.812
860.918
870.963
880.779
890.752
90.463
908.62297e-4
910.851
920.254
930.992
940.0403
950.507
960.0792
970.723
980.722
990.466



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: CNhs10583


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)
0000922 (embryo)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000302 (mouse embryonic day 18 sample)
0011513 (mouse lung- embryo E18 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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