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FF:354-16G2

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Name:lung, embryo E12
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stage12 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
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

CNhs10522

00
10
100
1000
10000
1001-0.0668
10020.194
1003-0.119
10040
1005-0.0389
1006-0.0351
10070.118
10080
1009-0.0045
1010.141
10100
10110
10120
1013-0.164
10140.339
10150.323
10160.26
10170
10180
10190
1020
10200
10210.14
1022-0.12
10230
1024-0.0298
10250.713
10260.0147
10270.107
10280
1029-0.107
1030
10300
10310.364
1032-0.108
10331.40711e-4
10340
10350
10360.162
10370
1038-0.0181
1039-0.157
1040
1040-0.016
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 no result for this sample


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: CNhs10522

Jaspar motifP-value
MA0002.20.0146
MA0003.10.673
MA0004.10.57
MA0006.10.549
MA0007.10.193
MA0009.10.373
MA0014.10.632
MA0017.11.42932e-4
MA0018.20.329
MA0019.10.897
MA0024.12.18435e-6
MA0025.10.728
MA0027.10.0148
MA0028.10.0211
MA0029.10.948
MA0030.10.421
MA0031.10.114
MA0035.20.296
MA0038.10.00568
MA0039.20.439
MA0040.10.684
MA0041.10.353
MA0042.10.357
MA0043.10.00569
MA0046.17.03748e-6
MA0047.20.534
MA0048.10.261
MA0050.11.16588e-6
MA0051.15.34885e-5
MA0052.10.138
MA0055.10.00987
MA0057.10.236
MA0058.10.284
MA0059.10.49
MA0060.11.51678e-16
MA0061.10.0837
MA0062.20.0515
MA0065.23.21981e-4
MA0066.10.0238
MA0067.10.46
MA0068.10.203
MA0069.10.914
MA0070.10.437
MA0071.10.134
MA0072.10.0481
MA0073.10.893
MA0074.10.396
MA0076.10.0311
MA0077.10.0938
MA0078.10.57
MA0079.20.365
MA0080.21.12909e-6
MA0081.10.606
MA0083.17.41234e-5
MA0084.10.224
MA0087.10.878
MA0088.10.649
MA0090.10.302
MA0091.10.689
MA0092.10.639
MA0093.10.49
MA0099.23.52694e-4
MA0100.10.57
MA0101.10.57
MA0102.20.595
MA0103.13.3923e-4
MA0104.20.339
MA0105.10.00262
MA0106.10.163
MA0107.10.318
MA0108.27.10597e-4
MA0111.10.268
MA0112.21.96819e-6
MA0113.10.583
MA0114.14.08906e-4
MA0115.10.0562
MA0116.10.00872
MA0117.10.192
MA0119.10.071
MA0122.10.599
MA0124.10.799
MA0125.10.139
MA0131.10.16
MA0135.10.102
MA0136.10.202
MA0137.20.421
MA0138.20.00169
MA0139.10.0801
MA0140.10.31
MA0141.10.0156
MA0142.10.404
MA0143.10.229
MA0144.10.445
MA0145.10.0332
MA0146.10.608
MA0147.10.411
MA0148.10.0717
MA0149.10.0183
MA0150.10.00727
MA0152.10.991
MA0153.10.00346
MA0154.10.00287
MA0155.10.823
MA0156.10.982
MA0157.10.161
MA0159.10.0286
MA0160.10.051
MA0162.10.574
MA0163.10.0803
MA0164.10.665
MA0258.11.66496e-4
MA0259.10.488



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: CNhs10522

Novel motifP-value
10.0554
100.27
1000.952
1010.636
1020.47
1030.0642
1040.859
1050.673
1060.017
1070.144
1080.978
1090.208
110.141
1100.284
1110.0178
1120.0316
1130.535
1140.00857
1150.783
1160.646
1170.36
1180.646
1190.0267
120.568
1200.449
1210.991
1220.907
1230.138
1240.263
1250.491
1260.585
1270.67
1280.0357
1290.0402
130.692
1300.171
1310.89
1320.376
1330.259
1340.587
1350.469
1360.547
1370.413
1380.859
1390.0021
140.276
1400.0153
1410.186
1420.397
1430.533
1440.771
1450.716
1460.568
1470.427
1480.0189
1490.383
150.0963
1500.539
1510.129
1520.167
1530.171
1540.24
1550.627
1563.11907e-5
1570.725
1580.335
1590.0391
1600.645
1610.556
1620.786
1630.161
1640.516
1650.537
1660.656
1670.467
1680.941
1690.018
170.0579
180.331
190.203
20.695
200.769
210.813
220.357
230.0324
240.858
250.406
260.57
270.233
280.249
290.553
30.0972
300.853
310.323
320.148
330.815
340.968
350.133
360.374
370.119
380.517
390.775
40.649
400.776
410.927
420.294
430.116
440.177
450.596
460.229
470.177
480.216
490.0909
50.13
500.812
510.588
520.461
530.736
540.44
550.83
560.324
570.397
580.259
590.366
60.4
600.158
610.506
620.0603
630.152
640.469
650.146
660.276
670.713
680.279
690.56
70.379
709.4056e-4
710.339
720.465
730.218
740.446
750.0751
760.984
770.197
780.244
790.517
80.245
800.463
810.325
820.0593
830.896
840.645
850.0114
860.527
870.432
880.998
890.307
90.555
900.0389
910.216
920.0864
930.364
940.199
950.368
960.365
970.313
980.127
990.804



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: CNhs10522


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
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000118 (lung bud)
0000119 (cell layer)
0000170 (pair of lungs)
0000171 (respiration organ)
0000310 (breast)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001443 (chest)
0001555 (digestive tract)
0002048 (lung)
0002050 (embryonic structure)
0002224 (thoracic cavity)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003258 (endoderm of foregut)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005153 (epithelial bud)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005423 (developing anatomical structure)
0005597 (lung primordium)
0005911 (endo-epithelium)
0007026 (primitive gut)
0008947 (respiratory primordium)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

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
NA

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