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FF:715-19A3: Difference between revisions

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|library_id=CNhs11111
|library_id=CNhs11111
|library_id_phase_based=1:CNhs11111
|name=lung, neonate N07
|name=lung, neonate N07
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 12:11, 18 June 2014


Name:lung, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11111
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stage7 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  DRS008902
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11111 CAGE DRX009039 DRR009913
Accession ID Mm9

Library idBAMCTSS
CNhs11111 DRZ001338 DRZ002721
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

CNhs11111

00
10
100
1000
10000.0869
10010.146
1002-0.0798
10030.327
10040
10050.048
10060.0764
10070.0873
10080
10090.446
101-0.0507
10100
1011-0.108
10120.0869
1013-0.0407
10140.231
1015-0.0272
10160.31
10170
10180.0869
10190
1020
10200
10210
10220.0353
10230
10240.717
10251.319
10260
10270
10280
10290.436
1030.276
10300.0869
10310.566
10320.0971
1033-0.022
10340.159
10350
10360.0101
10370
10380.598
10390.0755
1040
10400.502
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: CNhs11111

Jaspar motifP-value
MA0002.20.196
MA0003.10.123
MA0004.10.00899
MA0006.10.0156
MA0007.10.0448
MA0009.10.943
MA0014.10.96
MA0017.12.74956e-4
MA0018.22.01189e-4
MA0019.10.72
MA0024.10.82
MA0025.10.527
MA0027.10.367
MA0028.11.31617e-5
MA0029.10.504
MA0030.10.138
MA0031.10.169
MA0035.28.85344e-4
MA0038.10.879
MA0039.20.092
MA0040.10.817
MA0041.10.285
MA0042.10.525
MA0043.10.0156
MA0046.18.70528e-11
MA0047.20.00174
MA0048.10.466
MA0050.10.0124
MA0051.10.148
MA0052.10.586
MA0055.10.923
MA0057.10.701
MA0058.16.52627e-4
MA0059.17.10455e-4
MA0060.12.62165e-5
MA0061.10.533
MA0062.23.99855e-7
MA0065.20.00145
MA0066.10.162
MA0067.10.31
MA0068.10.882
MA0069.10.612
MA0070.10.482
MA0071.10.00975
MA0072.10.0287
MA0073.10.598
MA0074.10.734
MA0076.11.22032e-6
MA0077.10.182
MA0078.10.00523
MA0079.20.13
MA0080.20.03
MA0081.10.749
MA0083.11.54819e-4
MA0084.10.412
MA0087.10.232
MA0088.10.125
MA0090.10.051
MA0091.10.928
MA0092.10.789
MA0093.10.00497
MA0099.20.0422
MA0100.10.155
MA0101.10.735
MA0102.20.905
MA0103.10.0109
MA0104.21.3983e-5
MA0105.10.482
MA0106.10.018
MA0107.10.0586
MA0108.20.392
MA0111.10.684
MA0112.20.725
MA0113.10.827
MA0114.11.78766e-7
MA0115.10.00637
MA0116.10.571
MA0117.10.152
MA0119.10.0843
MA0122.10.325
MA0124.10.283
MA0125.10.124
MA0131.10.341
MA0135.10.354
MA0136.10.211
MA0137.20.184
MA0138.20.0425
MA0139.10.557
MA0140.10.292
MA0141.12.00246e-6
MA0142.10.735
MA0143.10.845
MA0144.10.825
MA0145.10.001
MA0146.10.892
MA0147.11.36997e-6
MA0148.10.0178
MA0149.10.817
MA0150.10.00268
MA0152.10.0457
MA0153.11.67719e-6
MA0154.10.158
MA0155.10.135
MA0156.10.976
MA0157.10.163
MA0159.10.00445
MA0160.14.12779e-5
MA0162.10.102
MA0163.10.206
MA0164.10.493
MA0258.10.129
MA0259.10.0141



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: CNhs11111

Novel motifP-value
10.422
100.302
1000.293
1010.806
1020.836
1030.887
1040.859
1050.753
1060.00179
1072.12936e-4
1080.765
1090.16
110.227
1100.423
1110.213
1120.911
1130.732
1140.138
1150.462
1160.892
1170.0168
1180.417
1190.898
120.627
1200.142
1210.733
1220.685
1230.62
1240.539
1250.914
1260.537
1270.529
1280.00916
1290.341
130.172
1300.0101
1310.118
1320.496
1330.501
1340.848
1350.159
1360.548
1370.329
1380.0347
1390.211
140.899
1400.659
1410.72
1420.457
1430.646
1440.511
1450.479
1460.709
1470.654
1480.687
1490.268
150.875
1500.0575
1510.769
1520.0916
1530.575
1540.0686
1550.711
1560.0228
1570.931
1580.864
1590.0459
1600.117
1610.817
1620.318
1630.81
1640.739
1650.35
1660.029
1670.504
1680.715
1690.0627
170.663
180.0201
190.0691
20.265
200.54
210.673
220.329
230.214
240.853
250.0423
260.146
270.641
280.661
290.111
30.42
300.815
310.499
320.134
330.569
340.589
350.0247
360.599
370.483
380.591
390.0882
40.841
400.985
410.258
420.714
430.488
440.0956
450.308
460.679
470.481
480.331
490.866
50.612
500.27
510.898
520.0415
530.6
540.753
550.797
560.953
570.567
580.514
590.31
60.872
600.102
610.586
620.225
630.794
640.201
650.879
660.135
670.877
680.294
690.636
70.98
700.0921
710.654
720.259
730.974
740.996
750.0633
760.994
770.55
780.182
790.82
80.158
800.271
810.144
820.726
830.908
840.164
850.54
860.733
877.91034e-4
880.736
890.672
90.324
900.0776
910.241
920.457
930.487
940.369
950.29
960.377
970.803
980.433
990.255



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: CNhs11111


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)
0000313 (mouse neonate N7 sample)
0011408 (mouse lung- neonate N07 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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