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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000118,UBERON:0000119,UBERON:0000170,UBERON:0000171,UBERON:0000310,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001443,UBERON:0001555,UBERON:0002048,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005153,UBERON:0005178,UBERON:0005181,UBERON:0005423,UBERON:0005482,UBERON:0005597,UBERON:0005911,UBERON:0007026,UBERON:0008947,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002048,UBERON:0000310,UBERON:0002100,UBERON:0000483,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000077,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005153,UBERON:0005911,UBERON:0004921,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0009569,UBERON:0005291,UBERON:0005178,UBERON:0005177,UBERON:0000117,UBERON:0000171,UBERON:0003104,UBERON:0000464,UBERON:0001048,UBERON:0000925,UBERON:0005181,UBERON:0006598,UBERON:0004185,UBERON:0005157,UBERON:0002532,UBERON:0001555,UBERON:0000065,UBERON:0000170,UBERON:0001004,UBERON:0001443,UBERON:0007026,UBERON:0001041,UBERON:0002224,UBERON:0000915,UBERON:0009142,UBERON:0008947,UBERON:0003258,UBERON:0005597,UBERON:0006595,UBERON:0006603,UBERON:0000118
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=

Revision as of 18:26, 8 June 2012


Name:lung, embryo E14
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 stage14 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

CNhs10604

00
10
100
1000
10000
10010.00899
10020.0933
10030.0305
10040
1005-0.161
1006-0.0795
10070.109
10080
10090.028
1010.166
10100
10110.0187
10120
1013-0.204
10140.305
10150.234
10160.297
10170
10180
10190
1020
10200
10210.0656
1022-0.0704
10230
10240.113
10251.005
10260
10270.0656
10280
10290.0704
1030.107
10300
10310.45
1032-0.0491
1033-0.0587
10340.0363
10350
10360
10370
10380.0479
1039-0.121
1040
10400.147
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: CNhs10604

Jaspar motifP-value
MA0002.25.71221e-4
MA0003.10.6
MA0004.10.939
MA0006.10.887
MA0007.10.22
MA0009.10.536
MA0014.10.288
MA0017.13.98691e-5
MA0018.20.629
MA0019.10.952
MA0024.11.71638e-8
MA0025.10.839
MA0027.10.00654
MA0028.10.167
MA0029.10.789
MA0030.10.854
MA0031.10.199
MA0035.20.261
MA0038.10.0492
MA0039.20.27
MA0040.10.784
MA0041.10.686
MA0042.10.36
MA0043.10.0925
MA0046.13.29288e-6
MA0047.20.497
MA0048.10.111
MA0050.11.01909e-7
MA0051.16.12085e-5
MA0052.10.274
MA0055.10.0152
MA0057.10.271
MA0058.10.83
MA0059.10.964
MA0060.17.51183e-11
MA0061.10.0879
MA0062.20.549
MA0065.22.03228e-4
MA0066.10.0166
MA0067.10.207
MA0068.10.738
MA0069.10.651
MA0070.10.911
MA0071.10.0117
MA0072.10.019
MA0073.10.774
MA0074.10.223
MA0076.10.263
MA0077.10.0841
MA0078.10.724
MA0079.20.657
MA0080.21.55564e-4
MA0081.10.799
MA0083.12.5374e-5
MA0084.10.864
MA0087.10.746
MA0088.10.55
MA0090.10.23
MA0091.10.612
MA0092.10.611
MA0093.10.883
MA0099.20.00141
MA0100.10.53
MA0101.10.606
MA0102.20.713
MA0103.10.00152
MA0104.20.59
MA0105.19.60888e-4
MA0106.10.704
MA0107.10.41
MA0108.20.853
MA0111.10.224
MA0112.27.23763e-6
MA0113.10.533
MA0114.11.19876e-4
MA0115.10.00376
MA0116.10.0303
MA0117.10.172
MA0119.10.263
MA0122.10.418
MA0124.10.694
MA0125.10.186
MA0131.10.174
MA0135.10.259
MA0136.10.0383
MA0137.20.0772
MA0138.24.62296e-4
MA0139.10.224
MA0140.10.873
MA0141.19.76102e-5
MA0142.10.979
MA0143.10.102
MA0144.10.352
MA0145.10.112
MA0146.10.838
MA0147.10.914
MA0148.10.911
MA0149.10.0104
MA0150.10.00227
MA0152.10.979
MA0153.17.22112e-4
MA0154.10.00279
MA0155.10.341
MA0156.10.794
MA0157.10.371
MA0159.10.00275
MA0160.10.00613
MA0162.10.728
MA0163.10.132
MA0164.10.983
MA0258.11.23654e-5
MA0259.10.733



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: CNhs10604

Novel motifP-value
10.0759
100.305
1000.973
1010.927
1020.593
1030.0662
1040.996
1050.668
1060.125
1070.269
1080.836
1090.113
110.0908
1100.26
1110.0252
1120.0589
1130.685
1140.00847
1150.493
1160.709
1170.337
1180.726
1190.0932
120.583
1200.084
1210.567
1220.786
1230.165
1240.549
1250.588
1260.723
1270.443
1280.093
1290.106
130.846
1300.0473
1310.542
1320.907
1330.321
1340.794
1350.918
1360.655
1370.796
1380.992
1390.00128
140.394
1400.0714
1410.355
1420.269
1430.551
1440.671
1450.744
1460.435
1470.305
1480.0555
1490.358
150.0828
1500.957
1510.0557
1520.242
1530.22
1540.707
1550.829
1565.57033e-4
1570.898
1580.816
1590.386
1600.86
1610.586
1620.766
1630.17
1640.645
1650.067
1660.19
1670.383
1680.87
1690.0676
170.0671
180.0804
190.462
20.814
200.754
210.838
220.548
230.0965
240.496
250.208
260.635
270.233
280.255
290.904
30.0623
300.735
310.3
320.0911
330.831
340.897
350.05
360.269
370.175
380.623
390.899
40.875
400.43
410.595
420.33
430.179
440.0146
450.509
460.375
470.173
480.14
490.116
50.193
500.675
510.554
520.64
530.779
540.318
550.961
560.257
570.405
580.218
590.241
60.503
600.303
610.944
620.0405
630.264
640.313
650.282
660.665
670.94
680.136
690.611
70.517
703.699e-4
710.482
720.224
730.116
740.801
750.118
760.769
770.227
780.397
790.635
80.124
800.273
810.107
820.101
830.55
840.819
850.0101
860.421
870.501
880.302
890.517
90.718
907.50611e-4
910.429
920.0263
930.648
940.288
950.344
960.144
970.314
980.201
990.587



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: CNhs10604


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
0000468 (multi-cellular organism)
0000922 (embryo)
0002048 (lung)
0000310 (breast)
0002100 (trunk)
0000483 (epithelium)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000077 (mixed endoderm/mesoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005153 (epithelial bud)
0005911 (endo-epithelium)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0003104 (mesenchyme)
0000464 (anatomical space)
0001048 (primordium)
0000925 (endoderm)
0005181 (thoracic segment organ)
0006598 (presumptive structure)
0004185 (endodermal part of digestive tract)
0005157 (epithelial fold)
0002532 (epiblast (generic))
0001555 (digestive tract)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0001443 (chest)
0007026 (primitive gut)
0001041 (foregut)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)
0009142 (entire embryonic mesenchyme)
0008947 (respiratory primordium)
0003258 (endoderm of foregut)
0005597 (lung primordium)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0000118 (lung bud)

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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