Personal tools

FF:1354-25G3

From FANTOM5_SSTAR

Revision as of 17:54, 25 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:spleen, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11099
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuespleen
dev stage25 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

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008952
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11099 CAGE DRX009089 DRR009963
Accession ID Mm9

Library idBAMCTSS
CNhs11099 DRZ001388 DRZ002771
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

CNhs11099

00
10
100
1000
10000
10010.00373
1002-0.00929
1003-0.0952
10040
10050.0895
1006-0.143
10070.0757
10080
1009-0.11
1010.109
10100
1011-0.018
10120.281
1013-0.0543
1014-0.0874
1015-0.0823
1016-0.333
10170
10180
10190
1020
10200
10210.0895
1022-0.171
10230
1024-0.117
10250
10260
10270
10280
10290.105
103-0.061
10300.842
1031-0.345
1032-0.324
10330.0971
10340
10350
10360.17
10370
1038-0.277
1039-0.185
1040
1040-0.121
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: CNhs11099

Jaspar motifP-value
MA0002.20.00606
MA0003.10.645
MA0004.10.723
MA0006.10.392
MA0007.10.812
MA0009.10.379
MA0014.10.624
MA0017.10.253
MA0018.20.0161
MA0019.10.258
MA0024.11.26292e-4
MA0025.10.126
MA0027.10.591
MA0028.10.0275
MA0029.10.741
MA0030.10.325
MA0031.10.929
MA0035.28.85354e-8
MA0038.10.094
MA0039.20.442
MA0040.10.687
MA0041.10.249
MA0042.10.825
MA0043.10.0049
MA0046.11.33357e-10
MA0047.20.945
MA0048.10.249
MA0050.12.32659e-13
MA0051.13.16512e-8
MA0052.14.80659e-5
MA0055.10.256
MA0057.10.671
MA0058.10.772
MA0059.10.175
MA0060.10.485
MA0061.12.44249e-4
MA0062.24.41613e-6
MA0065.20.222
MA0066.10.117
MA0067.10.917
MA0068.10.878
MA0069.10.754
MA0070.10.246
MA0071.10.727
MA0072.10.465
MA0073.10.804
MA0074.10.791
MA0076.10.0649
MA0077.10.103
MA0078.10.463
MA0079.20.0487
MA0080.27.98158e-12
MA0081.10.0235
MA0083.10.213
MA0084.10.406
MA0087.10.263
MA0088.10.169
MA0090.10.0474
MA0091.10.135
MA0092.10.79
MA0093.10.75
MA0099.20.636
MA0100.10.101
MA0101.15.6364e-4
MA0102.20.933
MA0103.10.999
MA0104.20.627
MA0105.16.56374e-7
MA0106.10.338
MA0107.16.24086e-4
MA0108.26.75158e-4
MA0111.10.581
MA0112.20.00191
MA0113.10.477
MA0114.10.81
MA0115.10.947
MA0116.10.00247
MA0117.10.772
MA0119.10.252
MA0122.10.708
MA0124.10.807
MA0125.10.0882
MA0131.10.913
MA0135.10.105
MA0136.12.72686e-14
MA0137.20.528
MA0138.20.0141
MA0139.10.175
MA0140.13.12822e-36
MA0141.10.517
MA0142.10.0302
MA0143.10.171
MA0144.10.73
MA0145.10.85
MA0146.10.226
MA0147.10.575
MA0148.10.728
MA0149.10.0287
MA0150.10.0491
MA0152.10.896
MA0153.11.82653e-6
MA0154.10.00235
MA0155.10.657
MA0156.13.68485e-12
MA0157.10.921
MA0159.10.0773
MA0160.10.944
MA0162.10.232
MA0163.11.00564e-4
MA0164.10.396
MA0258.10.0554
MA0259.10.971



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: CNhs11099

Novel motifP-value
10.0873
100.0265
1000.858
1010.947
1020.583
1030.0226
1040.973
1050.932
1060.204
1070.674
1080.333
1090.105
110.186
1100.0717
1110.0474
1120.0297
1130.727
1140.449
1150.522
1160.839
1177.74448e-4
1180.0875
1190.229
120.977
1200.621
1210.15
1220.911
1230.198
1240.888
1250.036
1260.188
1270.624
1280.258
1290.126
130.0109
1300.34
1310.815
1320.137
1330.391
1340.0972
1350.939
1360.954
1370.0308
1380.891
1390.563
140.64
1400.382
1410.487
1420.0501
1430.233
1440.905
1450.0344
1460.971
1470.783
1480.0932
1490.651
150.0407
1500.199
1510.25
1520.829
1530.357
1540.384
1550.101
1560.76
1570.989
1580.0449
1590.075
1600.598
1610.0604
1620.95
1630.299
1640.023
1650.202
1660.552
1670.0913
1680.641
1690.0277
170.349
180.193
190.355
20.262
200.052
210.338
220.539
230.954
240.267
250.268
260.00316
270.879
280.179
290.0333
30.0348
300.291
310.921
320.495
330.201
340.801
350.476
360.0419
370.138
380.49
390.894
40.936
400.204
410.757
420.0663
430.0766
440.609
450.738
460.148
470.181
480.21
490.0529
50.0932
500.997
510.828
520.905
530.892
540.886
550.307
560.506
570.128
580.332
590.352
60.547
600.368
610.277
620.134
630.403
640.623
650.417
660.708
670.535
680.21
690.357
70.0636
700.181
710.0255
720.211
730.29
740.759
750.0252
760.19
770.705
780.0247
790.797
80.0502
800.0458
810.391
820.669
830.336
840.0829
850.25
860.615
870.49
880.706
890.83
90.583
900.0256
910.18
920.676
930.478
940.0476
950.234
960.0146
970.885
980.154
990.676



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: CNhs11099


FANTOM5 (FF) ontology

Direct parent terms


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)
0002106 (spleen)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002323 (body cavity)
0005177 (trunk region element)
0004177 (hemopoietic organ)
0005057 (immune organ)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002390 (hematopoietic system)
0002417 (abdominal segment of trunk)
0002193 (hemolymphoid system)
0000916 (abdomen)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000309 (mouse neonate N25 sample)
0011491 (mouse spleen- neonate N25 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:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1354-25G3&oldid=3080339"