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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008900
|DRA_sample_Accession=CAGE@SAMD00004963
|accession_numbers=CAGE;DRX009037;DRR009911;DRZ001336;DRZ002719
|accession_numbers=CAGE;DRX009037;DRR009911;DRZ001336;DRZ002719
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002048,UBERON:0002100,UBERON:0000479,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0000464,UBERON:0005181,UBERON:0010317,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0002224,UBERON:0000915

Revision as of 21:58, 31 July 2014


Name:lung, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11224
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stage0 day 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  SAMD00004963
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11224 CAGE DRX009037 DRR009911
Accession ID Mm9

Library idBAMCTSS
CNhs11224 DRZ001336 DRZ002719
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

CNhs11224

00
10
100
1000
10000.00159
10010.15
10020.092
10030.065
10040
10050.143
10060
10070.157
10080
10090.395
101-0.0995
10100
1011-0.0976
10120.0926
10130.0846
10140.203
1015-0.0993
10160.36
10170
10180.251
10190
1020
10200
10210
10220.139
10230
10240.594
10251.122
10260
10270
10280.0774
10290.424
1030.198
10300
10310.433
10320.0236
10330
10340.164
10350.0774
1036-0.151
10370
10380.42
1039-0.0351
1040
10400.491
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: CNhs11224

Jaspar motifP-value
MA0002.20.101
MA0003.10.319
MA0004.10.0398
MA0006.10.0401
MA0007.10.809
MA0009.10.807
MA0014.10.916
MA0017.14.4892e-4
MA0018.20.00905
MA0019.10.701
MA0024.13.20136e-4
MA0025.10.726
MA0027.10.442
MA0028.13.07922e-4
MA0029.10.952
MA0030.10.0302
MA0031.12.95792e-4
MA0035.20.338
MA0038.10.523
MA0039.20.0771
MA0040.10.8
MA0041.10.304
MA0042.10.654
MA0043.10.533
MA0046.17.94682e-4
MA0047.24.78816e-8
MA0048.10.486
MA0050.10.181
MA0051.10.165
MA0052.10.458
MA0055.10.198
MA0057.10.727
MA0058.10.00647
MA0059.12.10902e-4
MA0060.14.65224e-6
MA0061.10.544
MA0062.24.03486e-5
MA0065.20.0106
MA0066.10.0677
MA0067.10.78
MA0068.10.544
MA0069.10.484
MA0070.10.521
MA0071.10.0261
MA0072.10.133
MA0073.10.574
MA0074.10.755
MA0076.12.43981e-4
MA0077.10.545
MA0078.10.0302
MA0079.20.0164
MA0080.20.7
MA0081.10.797
MA0083.12.33364e-4
MA0084.10.515
MA0087.10.465
MA0088.10.0412
MA0090.10.00879
MA0091.10.39
MA0092.10.836
MA0093.10.0393
MA0099.20.695
MA0100.10.314
MA0101.10.974
MA0102.20.156
MA0103.10.746
MA0104.29.46635e-5
MA0105.10.0172
MA0106.10.157
MA0107.10.169
MA0108.20.0246
MA0111.10.77
MA0112.20.131
MA0113.10.357
MA0114.17.62592e-6
MA0115.10.0694
MA0116.10.0159
MA0117.10.259
MA0119.10.386
MA0122.10.49
MA0124.10.128
MA0125.10.522
MA0131.10.29
MA0135.10.708
MA0136.10.0111
MA0137.20.43
MA0138.20.239
MA0139.10.391
MA0140.10.976
MA0141.18.72131e-5
MA0142.10.031
MA0143.10.103
MA0144.10.61
MA0145.10.0189
MA0146.10.312
MA0147.11.59698e-5
MA0148.14.07844e-6
MA0149.10.733
MA0150.10.00399
MA0152.10.362
MA0153.13.68861e-4
MA0154.10.92
MA0155.10.349
MA0156.10.441
MA0157.10.0395
MA0159.10.0214
MA0160.10.00239
MA0162.10.768
MA0163.10.00704
MA0164.10.501
MA0258.10.129
MA0259.10.0444



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: CNhs11224

Novel motifP-value
10.258
100.0558
1000.309
1010.62
1020.279
1030.466
1040.942
1050.785
1060.0123
1070.00392
1080.997
1090.462
110.209
1100.294
1110.274
1120.512
1130.539
1140.669
1150.445
1160.395
1170.0575
1180.893
1190.906
120.632
1200.171
1210.567
1220.96
1230.862
1240.784
1250.99
1260.458
1270.252
1280.0395
1291
130.154
1300.148
1310.221
1320.258
1330.808
1340.922
1350.887
1360.214
1370.648
1380.0139
1390.274
140.992
1400.323
1410.336
1420.595
1430.158
1440.703
1450.211
1460.752
1470.257
1480.583
1490.409
150.536
1500.117
1510.455
1520.0117
1530.517
1540.579
1550.99
1560.656
1570.785
1580.363
1590.0495
1600.593
1610.75
1620.394
1630.289
1640.743
1650.336
1660.431
1670.163
1680.391
1690.445
170.938
180.00693
190.365
20.31
200.841
210.632
220.266
230.281
240.644
250.0183
260.695
270.255
280.995
290.0557
30.503
300.676
310.498
320.341
330.757
340.951
350.00429
360.313
370.387
380.928
390.0816
40.402
400.868
410.352
420.572
430.966
440.146
450.296
460.323
470.16
480.169
490.589
50.508
500.279
510.886
520.0467
530.944
540.935
550.598
560.888
570.242
580.424
590.513
60.468
600.101
610.817
620.151
630.878
640.107
650.987
660.117
670.884
680.436
690.799
70.895
700.404
710.109
720.157
730.196
740.566
750.0745
760.957
770.273
780.559
790.832
80.114
800.317
810.00889
820.424
830.408
840.594
850.914
860.984
870.00499
880.841
890.361
90.354
900.00225
910.386
920.775
930.782
940.031
950.539
960.159
970.553
980.28
990.807



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: CNhs11224


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)
0000304 (mouse neonate N0 sample)
0011394 (mouse lung- neonate N00 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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