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{{f5samples
{{f5samples
|id=FF:480-44A6
|id=FF:480-44A6
|name=lung, embryo E17, biol_rep1
|name=lung, embryo E17
|sample_id=480
|sample_id=480
|rna_tube_id=480-44A6
|rna_tube_id=44A6
|rna_box=480-44A6
|rna_box=44
|rna_position=480-44A6
|rna_position=A6
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
Line 32: Line 32:
|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs10605,LSID654,,COMPLETED
|profile_hcage=CNhs10605,LSID654,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:41, 27 February 2012


Name:lung, embryo E17
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 stage17 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]





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

CNhs10605

00
10
100
1000
10000
10010.0528
1002-0.0818
10030.0942
10040
10050.0652
10060
10070.0934
10080
10090.169
101-0.0221
10100
10110.045
10120
1013-0.0819
10140.177
10150.0347
10160.25
10170
10180.108
10190
1020
10200
10210
10220.0673
10230
10240.337
10251.211
10260
10270
10280
10290.203
1030.0673
10300
10310.492
1032-0.0204
10330
10340
10350.0673
1036-0.0187
10370
10380.373
10390.0209
1040
10400.313
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: CNhs10605

Jaspar motifP-value
MA0002.20.0446
MA0003.10.117
MA0004.10.171
MA0006.10.201
MA0007.10.337
MA0009.10.673
MA0014.10.789
MA0017.12.35709e-6
MA0018.20.216
MA0019.10.468
MA0024.10.00484
MA0025.10.402
MA0027.10.445
MA0028.10.839
MA0029.10.768
MA0030.10.0822
MA0031.10.115
MA0035.20.0188
MA0038.10.187
MA0039.20.013
MA0040.10.607
MA0041.10.693
MA0042.10.463
MA0043.10.316
MA0046.11.93014e-5
MA0047.27.53659e-7
MA0048.10.526
MA0050.10.623
MA0051.10.855
MA0052.10.135
MA0055.10.0351
MA0057.10.899
MA0058.10.103
MA0059.10.00225
MA0060.14.00437e-4
MA0061.10.531
MA0062.20.848
MA0065.20.00125
MA0066.10.0104
MA0067.10.273
MA0068.10.729
MA0069.10.805
MA0070.10.266
MA0071.10.0137
MA0072.10.0845
MA0073.10.623
MA0074.10.137
MA0076.10.798
MA0077.10.843
MA0078.10.0288
MA0079.20.0216
MA0080.20.418
MA0081.10.505
MA0083.15.71507e-4
MA0084.10.774
MA0087.10.969
MA0088.10.589
MA0090.10.00417
MA0091.10.178
MA0092.10.671
MA0093.10.212
MA0099.20.0307
MA0100.10.754
MA0101.10.846
MA0102.20.32
MA0103.10.208
MA0104.20.00299
MA0105.10.00169
MA0106.10.67
MA0107.10.391
MA0108.20.613
MA0111.10.628
MA0112.27.93069e-4
MA0113.10.959
MA0114.13.04359e-6
MA0115.10.00194
MA0116.10.0156
MA0117.10.0232
MA0119.10.681
MA0122.10.193
MA0124.10.291
MA0125.10.506
MA0131.10.746
MA0135.10.22
MA0136.10.816
MA0137.20.84
MA0138.20.00523
MA0139.10.856
MA0140.10.148
MA0141.14.77937e-6
MA0142.10.162
MA0143.10.801
MA0144.10.982
MA0145.10.0641
MA0146.10.5
MA0147.16.52325e-4
MA0148.19.28319e-5
MA0149.10.232
MA0150.11.23925e-4
MA0152.10.876
MA0153.13.77621e-4
MA0154.10.193
MA0155.10.187
MA0156.10.0515
MA0157.10.457
MA0159.10.00269
MA0160.10.00267
MA0162.10.6
MA0163.10.0138
MA0164.10.335
MA0258.19.62163e-5
MA0259.10.378



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: CNhs10605

Novel motifP-value
10.0706
100.127
1000.483
1010.926
1020.993
1030.139
1040.791
1050.811
1060.737
1070.703
1080.858
1090.254
110.126
1100.34
1110.0214
1120.144
1130.905
1140.0141
1150.318
1160.846
1170.0284
1180.442
1190.13
120.468
1200.104
1210.312
1220.853
1230.569
1240.684
1250.991
1260.998
1270.397
1280.517
1290.321
130.113
1300.00281
1310.63
1320.749
1330.727
1340.689
1350.602
1360.195
1370.455
1380.607
1390.00676
140.739
1400.0278
1410.262
1420.22
1430.257
1440.395
1450.478
1460.989
1470.378
1480.069
1490.53
150.123
1500.331
1510.131
1520.0916
1530.214
1540.772
1550.874
1560.0397
1570.802
1580.794
1590.032
1600.335
1610.897
1620.875
1630.174
1640.287
1650.235
1660.415
1670.0162
1680.947
1690.869
170.214
180.00507
190.92
20.678
200.615
210.805
220.651
230.703
240.599
250.144
260.979
270.567
280.799
290.206
30.205
300.614
310.115
320.00507
330.66
340.775
350.00257
360.234
370.8
380.836
390.619
40.74
400.909
410.39
420.489
430.14
440.0383
450.429
460.149
470.205
480.222
490.0539
50.278
500.322
510.491
520.448
530.666
540.326
550.906
560.528
570.158
580.478
590.929
60.593
600.753
610.754
620.0968
630.75
640.2
650.474
660.941
670.941
680.0264
690.572
70.99
700.00362
710.322
720.27
730.77
740.965
750.0333
760.627
770.708
780.257
790.833
80.0392
800.772
810.0354
820.0821
830.114
840.51
850.129
860.723
870.378
880.766
890.439
90.624
900.00162
910.476
920.0349
930.59
940.0201
950.772
960.0552
970.784
980.453
990.959



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: CNhs10605


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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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