Personal tools

FF:458-17B6

From FANTOM5_SSTAR

Revision as of 14:14, 27 January 2012 by Autoedit (talk | contribs) (Created page with "{{f5samples |id=FF:458-17B6 |name=lung, embryo E16, biol_rep1 |sample_id=458 |rna_tube_id=458-17B6 |rna_box=458-17B6 |rna_position=458-17B6 |sample_cell_lot= |sample_c...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:lung, embryo E16, biol_rep1
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 stage16 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

CNhs10998

00
10
100
1000
10000.0577
10010.0168
10020.0363
10030.0915
10040
1005-0.0818
1006-0.143
10070.109
10080
10090.213
1010.0608
10100
10110
10120
1013-0.128
10140.487
10150.154
10160.2
10170
10180
10190
1020
10200
10210
10220.0916
10230
10240.0746
10251.121
10260
10270
10280
10290.283
1030.147
10300
10310.391
1032-0.00941
10330.0503
10340.0916
10350
10360.194
10370
10380.125
1039-0.117
1040
10400.253
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: CNhs10998

Jaspar motifP-value
MA0002.20.00173
MA0003.10.492
MA0004.10.467
MA0006.10.881
MA0007.10.594
MA0009.10.748
MA0014.10.442
MA0017.14.21473e-5
MA0018.20.0141
MA0019.10.403
MA0024.12.66236e-8
MA0025.10.165
MA0027.10.165
MA0028.10.203
MA0029.10.651
MA0030.10.693
MA0031.10.227
MA0035.21.03672e-4
MA0038.10.464
MA0039.20.206
MA0040.10.548
MA0041.10.215
MA0042.10.351
MA0043.10.47
MA0046.11.03235e-8
MA0047.20.281
MA0048.12.32686e-4
MA0050.10.033
MA0051.10.0061
MA0052.10.0114
MA0055.11.66934e-4
MA0057.10.371
MA0058.10.242
MA0059.10.866
MA0060.10.00453
MA0061.10.14
MA0062.20.859
MA0065.22.31151e-4
MA0066.10.149
MA0067.10.0951
MA0068.10.949
MA0069.10.611
MA0070.10.719
MA0071.10.0169
MA0072.10.00772
MA0073.10.596
MA0074.10.301
MA0076.10.615
MA0077.10.677
MA0078.10.317
MA0079.20.15
MA0080.23.11992e-4
MA0081.10.386
MA0083.10.12
MA0084.10.555
MA0087.10.389
MA0088.10.655
MA0090.10.201
MA0091.10.837
MA0092.10.985
MA0093.10.439
MA0099.21.40392e-5
MA0100.10.385
MA0101.10.46
MA0102.20.848
MA0103.10.0143
MA0104.20.316
MA0105.10.178
MA0106.10.137
MA0107.10.355
MA0108.20.00292
MA0111.10.609
MA0112.20.0578
MA0113.10.425
MA0114.18.26718e-6
MA0115.10.00629
MA0116.10.98
MA0117.10.00681
MA0119.10.465
MA0122.10.733
MA0124.10.533
MA0125.10.902
MA0131.10.305
MA0135.10.166
MA0136.14.77776e-4
MA0137.20.13
MA0138.28.09726e-6
MA0139.10.928
MA0140.10.0384
MA0141.13.31588e-4
MA0142.10.433
MA0143.10.491
MA0144.10.234
MA0145.10.414
MA0146.10.557
MA0147.10.304
MA0148.10.622
MA0149.10.33
MA0150.11.375e-5
MA0152.10.568
MA0153.14.75115e-5
MA0154.10.148
MA0155.10.162
MA0156.10.203
MA0157.10.34
MA0159.10.00533
MA0160.11.27878e-4
MA0162.10.602
MA0163.10.664
MA0164.10.97
MA0258.10.00455
MA0259.10.63



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: CNhs10998

Novel motifP-value
10.159
100.701
1000.587
1010.964
1020.63
1030.857
1040.429
1050.749
1060.54
1070.806
1080.618
1090.223
110.16
1100.983
1110.145
1120.239
1130.469
1140.0588
1150.496
1160.932
1170.857
1180.924
1190.199
120.421
1200.158
1210.766
1220.76
1230.323
1240.778
1250.471
1260.56
1270.552
1280.502
1290.121
130.00651
1300.0175
1310.707
1320.876
1330.648
1340.417
1350.417
1360.674
1370.793
1380.291
1390.0143
140.291
1400.778
1410.497
1420.867
1430.55
1440.836
1450.672
1460.108
1470.596
1480.154
1490.84
150.203
1500.341
1510.0469
1520.256
1530.502
1540.413
1550.566
1560.029
1570.877
1580.785
1590.0259
1600.134
1610.822
1620.932
1630.0247
1640.621
1650.266
1660.182
1670.603
1680.7
1690.853
170.197
180.0242
190.734
20.409
200.397
210.36
220.674
230.159
240.819
250.149
260.0639
270.147
280.366
290.531
30.568
300.536
310.17
320.058
330.846
340.775
350.118
360.537
370.743
380.912
390.301
40.761
400.504
410.193
420.926
430.38
440.0318
450.26
460.569
470.353
480.208
490.229
50.606
500.442
510.694
520.947
530.698
540.229
550.814
560.374
570.85
580.464
590.439
60.629
600.815
610.602
620.0975
630.572
640.373
650.298
660.717
670.499
680.202
690.699
70.903
700.00497
710.452
720.0764
730.149
740.647
750.404
760.391
770.293
780.209
790.83
80.391
800.111
810.029
820.288
830.665
840.0745
850.0812
860.577
870.00203
880.338
890.213
90.886
900.0827
910.988
920.0724
930.728
940.423
950.65
960.402
970.173
980.343
990.879



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: CNhs10998


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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:458-17B6&oldid=7101"