Personal tools

FF:683-20E5: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:683-20E5
|id=FF:683-20E5
|name=lung, neonate N06, biol_rep1
|name=lung, neonate N06
|sample_id=683
|sample_id=683
|rna_tube_id=683-20E5
|rna_tube_id=20E5
|rna_box=683-20E5
|rna_box=20
|rna_position=683-20E5
|rna_position=E5
|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=CNhs11212,LSID747,,COMPLETED
|profile_hcage=CNhs11212,LSID747,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:41, 27 February 2012


Name:lung, neonate N06
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 stage6 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
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

CNhs11212

00
10
100
1000
10000.0318
10010.145
1002-0.0623
10030.15
10040
10050.173
10060.0636
10070.147
10080.0636
10090.428
101-0.0207
10100
1011-0.0142
10120.0636
1013-0.0195
10140.0831
1015-0.012
10160.205
10170
10180
10190
1020
10200
1021-0.00561
10220.0999
10230
10240.594
10251.285
10260
10270
10280
10290.487
1030.187
10300.0636
10310.568
10320.0549
10330
10340.168
10350
1036-0.0446
10370
10380.567
1039-0.049
1040
10400.531
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: CNhs11212

Jaspar motifP-value
MA0002.20.319
MA0003.10.1
MA0004.10.0135
MA0006.10.0349
MA0007.10.0535
MA0009.10.954
MA0014.10.933
MA0017.14.11734e-5
MA0018.20.00367
MA0019.10.562
MA0024.10.43
MA0025.10.866
MA0027.10.422
MA0028.10.00136
MA0029.10.9
MA0030.10.0159
MA0031.10.0245
MA0035.20.107
MA0038.10.893
MA0039.20.026
MA0040.10.471
MA0041.10.311
MA0042.10.487
MA0043.10.359
MA0046.11.07895e-9
MA0047.21.32094e-5
MA0048.10.756
MA0050.10.0368
MA0051.10.12
MA0052.10.0914
MA0055.10.607
MA0057.10.755
MA0058.10.00161
MA0059.14.31961e-5
MA0060.10.00787
MA0061.10.702
MA0062.20.00184
MA0065.20.00135
MA0066.10.0362
MA0067.10.497
MA0068.10.755
MA0069.10.757
MA0070.10.909
MA0071.10.00317
MA0072.10.0436
MA0073.10.669
MA0074.10.273
MA0076.18.7368e-4
MA0077.10.342
MA0078.10.00816
MA0079.20.065
MA0080.22.35562e-4
MA0081.10.281
MA0083.12.88279e-6
MA0084.10.741
MA0087.10.546
MA0088.10.284
MA0090.10.0129
MA0091.10.477
MA0092.10.746
MA0093.10.00993
MA0099.20.0535
MA0100.10.493
MA0101.10.477
MA0102.20.451
MA0103.10.0122
MA0104.26.0077e-5
MA0105.10.0343
MA0106.10.146
MA0107.10.0334
MA0108.20.831
MA0111.10.913
MA0112.20.0744
MA0113.10.613
MA0114.17.53432e-7
MA0115.10.00506
MA0116.10.0328
MA0117.10.207
MA0119.10.378
MA0122.10.172
MA0124.10.144
MA0125.10.325
MA0131.10.512
MA0135.10.801
MA0136.10.476
MA0137.20.579
MA0138.20.132
MA0139.10.9
MA0140.10.344
MA0141.14.52091e-7
MA0142.10.341
MA0143.10.951
MA0144.10.649
MA0145.10.00304
MA0146.10.928
MA0147.13.5889e-6
MA0148.11.07242e-4
MA0149.10.65
MA0150.10.00202
MA0152.10.667
MA0153.11.05985e-5
MA0154.10.625
MA0155.10.301
MA0156.10.0428
MA0157.10.0365
MA0159.15.84476e-4
MA0160.11.31606e-4
MA0162.10.506
MA0163.10.00225
MA0164.10.312
MA0258.10.0112
MA0259.10.0233



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: CNhs11212

Novel motifP-value
10.244
100.0844
1000.191
1010.553
1020.731
1030.502
1040.696
1050.884
1060.0892
1070.00666
1080.659
1090.155
110.0952
1100.231
1110.0658
1120.614
1130.873
1140.0883
1150.411
1160.399
1170.0103
1180.346
1190.862
120.46
1200.0954
1210.231
1220.81
1230.65
1240.352
1250.531
1260.861
1270.633
1280.0997
1290.58
130.449
1300.012
1310.0359
1320.808
1330.628
1340.508
1350.302
1360.981
1370.244
1380.149
1390.184
140.807
1400.464
1410.822
1420.696
1430.393
1440.712
1450.88
1460.921
1470.46
1480.821
1490.264
150.513
1500.365
1510.844
1520.122
1530.766
1540.489
1550.705
1560.00113
1570.868
1580.832
1590.0353
1600.258
1610.592
1620.333
1630.84
1640.727
1650.367
1660.153
1670.354
1680.973
1690.305
170.463
180.00535
190.152
20.162
200.189
210.924
220.402
230.221
240.725
250.177
260.619
270.715
280.769
290.0569
30.235
300.568
310.422
320.121
330.593
340.495
350.00563
360.369
370.958
380.563
390.183
40.78
400.988
410.331
420.625
430.706
440.0272
450.256
460.388
470.301
480.225
490.244
50.653
500.405
510.893
520.12
530.362
540.943
550.827
560.745
570.308
580.741
590.54
60.746
600.199
610.692
620.278
630.967
640.113
650.859
660.181
670.887
680.174
690.532
70.84
700.0257
710.178
720.258
730.628
740.945
750.0201
760.5
770.564
780.155
790.772
80.0642
800.658
810.14
820.403
830.823
840.494
850.886
860.761
870.0083
880.609
890.674
90.336
900.0126
910.662
920.52
930.472
940.344
950.351
960.328
970.696
980.582
990.353



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: CNhs11212


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)
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)
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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:683-20E5&oldid=416836"