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|library_id=CNhs11133
|library_id=CNhs11133
|library_id_phase_based=1:CNhs11133
|name=lung, neonate N30
|name=lung, neonate N30
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:12, 18 June 2014


Name:lung, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11133
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stage30 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  DRS008906
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11133 CAGE DRX009043 DRR009917
Accession ID Mm9

Library idBAMCTSS
CNhs11133 DRZ001342 DRZ002725
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

CNhs11133

00
10
100
1000
10000.0569
10010.244
10020.0331
10030.112
10040
10050.166
10060.0139
10070.0371
10080
10090.399
101-0.132
10100
1011-0.0958
10120.0598
10130.0242
10140.0174
1015-0.155
10160.0634
10170
10180.0461
10190
1020
10200
10210.0444
10220.157
10230
10240.608
10251.238
10260
10270
10280
10290.247
1030.0913
10300.236
10310.29
10320.106
10330
10340.437
10350.0375
1036-0.153
10370.00849
10380.481
10390.101
1040
10400.527
10410.271



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: CNhs11133

Jaspar motifP-value
MA0002.20.429
MA0003.10.122
MA0004.10.0425
MA0006.10.0251
MA0007.10.92
MA0009.10.637
MA0014.10.684
MA0017.10.131
MA0018.22.40091e-4
MA0019.10.816
MA0024.12.83067e-5
MA0025.10.232
MA0027.10.336
MA0028.10.00816
MA0029.10.422
MA0030.10.0538
MA0031.12.3186e-4
MA0035.20.197
MA0038.10.82
MA0039.20.00134
MA0040.10.436
MA0041.10.333
MA0042.10.577
MA0043.10.0873
MA0046.18.42748e-8
MA0047.24.6797e-7
MA0048.10.887
MA0050.15.32429e-8
MA0051.13.98371e-5
MA0052.10.985
MA0055.10.829
MA0057.10.311
MA0058.10.0307
MA0059.10.0112
MA0060.14.38761e-7
MA0061.10.127
MA0062.20.0247
MA0065.20.559
MA0066.10.495
MA0067.10.903
MA0068.10.0996
MA0069.10.65
MA0070.10.804
MA0071.10.505
MA0072.10.423
MA0073.10.826
MA0074.10.558
MA0076.10.0038
MA0077.10.0413
MA0078.14.82441e-4
MA0079.20.0067
MA0080.26.1009e-8
MA0081.10.247
MA0083.10.159
MA0084.10.7
MA0087.10.959
MA0088.10.861
MA0090.10.0232
MA0091.10.773
MA0092.10.646
MA0093.10.0366
MA0099.20.841
MA0100.10.228
MA0101.10.178
MA0102.20.216
MA0103.10.821
MA0104.24.91083e-4
MA0105.10.876
MA0106.10.0288
MA0107.10.00519
MA0108.20.149
MA0111.10.523
MA0112.20.126
MA0113.10.133
MA0114.10.00868
MA0115.10.253
MA0116.10.705
MA0117.10.651
MA0119.10.0473
MA0122.10.27
MA0124.10.79
MA0125.10.103
MA0131.10.212
MA0135.10.831
MA0136.10.00591
MA0137.20.395
MA0138.20.507
MA0139.10.122
MA0140.10.644
MA0141.10.0146
MA0142.10.83
MA0143.10.239
MA0144.10.0989
MA0145.15.45955e-4
MA0146.10.22
MA0147.11.07828e-4
MA0148.19.93415e-6
MA0149.10.554
MA0150.10.264
MA0152.10.356
MA0153.11.04493e-5
MA0154.10.0207
MA0155.10.288
MA0156.13.23465e-4
MA0157.10.00121
MA0159.10.293
MA0160.10.054
MA0162.10.342
MA0163.10.461
MA0164.10.492
MA0258.10.606
MA0259.10.00327



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: CNhs11133

Novel motifP-value
10.925
100.529
1000.459
1010.56
1020.422
1030.368
1040.639
1050.413
1064.94388e-4
1070.0038
1080.638
1090.284
110.977
1100.949
1110.416
1120.46
1130.758
1140.783
1150.476
1160.632
1170.172
1180.82
1190.131
120.612
1200.158
1210.24
1220.838
1230.921
1240.585
1250.492
1260.332
1270.66
1280.00271
1290.187
130.00295
1300.00362
1310.0305
1320.367
1330.757
1340.678
1350.745
1360.901
1370.455
1380.0462
1390.987
140.283
1400.951
1410.391
1420.194
1430.364
1440.984
1450.187
1460.626
1470.738
1480.189
1490.0733
150.348
1500.136
1510.282
1520.0161
1530.455
1540.245
1550.773
1560.00683
1570.737
1580.974
1590.108
1600.16
1610.67
1620.459
1630.748
1640.649
1650.935
1660.115
1670.367
1680.26
1690.0187
170.467
180.0507
190.0628
20.104
200.503
210.578
220.0965
230.0358
240.241
250.124
260.0714
270.913
280.518
290.408
30.602
300.73
310.865
320.62
330.974
340.502
350.0661
360.813
370.0529
380.163
390.0757
40.818
400.623
410.291
420.647
430.162
440.301
450.118
460.911
470.941
480.898
490.263
50.806
500.338
510.665
520.031
530.483
540.743
550.941
560.508
570.838
580.838
590.143
60.996
600.0289
610.855
620.844
630.217
640.436
650.127
660.114
670.878
680.818
690.982
70.503
700.45
710.74
720.922
730.107
740.813
750.46
760.768
770.203
780.792
790.871
80.49
800.897
810.48
820.563
830.476
840.141
850.0754
860.922
870.114
880.46
890.996
90.174
900.617
910.365
920.255
930.44
940.34
950.641
960.828
970.428
980.745
990.211



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: CNhs11133


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)
0000310 (mouse neonate N30 sample)
0011489 (mouse lung- neonate N30 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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