Personal tools

FF:1541-43F8

From FANTOM5_SSTAR

Revision as of 19:08, 4 June 2020 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:thymus, neonate N02
Species:Mouse (Mus musculus)
Library ID:CNhs11181
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage2 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  SAMD00004748
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11181 CAGE DRX009118 DRR009992
Accession ID Mm9

Library idBAMCTSS
CNhs11181 DRZ001417 DRZ002800
Accession ID Mm10

Library idBAMCTSS
CNhs11181 DRZ012767 DRZ014150
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11181

00
10
100
1000
10000
10010.0133
1002-4.923381e-4
1003-0.0929
10040
10050
1006-0.0934
10070.102
10080.0493
1009-0.109
1010.134
10100
10110.0433
10120.429
1013-0.12
1014-0.0851
10150.121
1016-0.276
10170
10180.134
10190
1020.0493
10200
10210.218
1022-0.249
10230
10240.00111
1025-0.0611
10260
10270
10280
10290.252
103-0.0402
10300
1031-0.529
1032-0.39
10330.0493
10340
10350
10360.161
10370
1038-0.419
1039-0.225
1040
1040-0.121
10410.0493



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: CNhs11181

Jaspar motifP-value
MA0002.20.00351
MA0003.10.358
MA0004.10.339
MA0006.10.971
MA0007.10.475
MA0009.10.37
MA0014.10.168
MA0017.10.568
MA0018.20.0268
MA0019.10.44
MA0024.11.1952e-5
MA0025.10.00169
MA0027.10.553
MA0028.14.20465e-6
MA0029.10.171
MA0030.10.528
MA0031.10.441
MA0035.20.378
MA0038.10.666
MA0039.20.234
MA0040.10.703
MA0041.10.247
MA0042.10.92
MA0043.10.0624
MA0046.16.31016e-17
MA0047.20.666
MA0048.10.442
MA0050.17.33911e-7
MA0051.18.38286e-6
MA0052.10.00211
MA0055.10.955
MA0057.10.679
MA0058.10.564
MA0059.10.0112
MA0060.10.0272
MA0061.11.75287e-5
MA0062.21.45774e-16
MA0065.20.595
MA0066.10.01
MA0067.10.687
MA0068.10.591
MA0069.10.96
MA0070.10.381
MA0071.10.406
MA0072.18.76734e-6
MA0073.10.813
MA0074.10.893
MA0076.12.2603e-7
MA0077.10.123
MA0078.10.835
MA0079.20.0302
MA0080.22.69867e-13
MA0081.10.0202
MA0083.10.111
MA0084.10.422
MA0087.10.391
MA0088.10.427
MA0090.10.0909
MA0091.10.0341
MA0092.10.871
MA0093.10.39
MA0099.20.139
MA0100.10.0148
MA0101.12.76991e-5
MA0102.20.422
MA0103.19.25475e-5
MA0104.20.0944
MA0105.14.66804e-8
MA0106.10.75
MA0107.15.01618e-5
MA0108.20.00501
MA0111.10.206
MA0112.20.0123
MA0113.10.655
MA0114.10.247
MA0115.10.551
MA0116.10.00299
MA0117.10.589
MA0119.10.797
MA0122.10.987
MA0124.10.33
MA0125.10.548
MA0131.10.0874
MA0135.10.262
MA0136.11.71989e-21
MA0137.20.0646
MA0138.23.92394e-6
MA0139.10.195
MA0140.10.498
MA0141.10.357
MA0142.10.712
MA0143.10.272
MA0144.10.249
MA0145.10.45
MA0146.10.411
MA0147.10.0345
MA0148.10.582
MA0149.10.0418
MA0150.10.335
MA0152.10.762
MA0153.12.13701e-8
MA0154.10.131
MA0155.10.799
MA0156.15.86625e-25
MA0157.10.458
MA0159.10.101
MA0160.10.242
MA0162.10.421
MA0163.11.96536e-4
MA0164.10.717
MA0258.10.0315
MA0259.10.678



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: CNhs11181

Novel motifP-value
10.23
100.0104
1000.766
1011
1020.48
1030.188
1040.906
1050.894
1060.676
1070.951
1080.236
1090.3
110.121
1100.0464
1110.671
1120.141
1130.392
1140.942
1150.446
1160.732
1179.46648e-4
1180.172
1190.328
120.65
1200.185
1210.423
1220.64
1230.675
1240.78
1250.119
1260.579
1270.975
1280.604
1290.199
130.0124
1300.193
1310.549
1320.7
1330.66
1340.484
1350.44
1360.571
1370.34
1380.766
1390.556
140.685
1400.794
1410.977
1420.705
1430.161
1440.171
1450.0566
1460.889
1470.291
1480.378
1490.836
150.103
1500.306
1510.278
1520.0793
1530.221
1540.0751
1550.146
1560.00315
1570.384
1580.164
1590.0697
1600.926
1610.315
1620.632
1630.759
1640.118
1650.273
1660.305
1670.145
1680.353
1690.331
170.665
180.743
190.673
20.0685
200.216
210.365
220.947
230.843
240.147
250.235
260.0169
270.528
280.276
290.0446
30.153
300.11
310.458
320.117
330.358
340.914
350.0987
360.158
370.257
380.229
390.983
40.813
400.503
410.988
420.0329
430.47
440.849
450.83
460.102
470.434
480.227
490.185
50.345
500.922
510.877
520.198
530.837
540.329
550.345
560.923
570.226
580.249
590.836
60.251
600.964
610.0523
620.095
630.538
640.747
650.51
660.593
670.647
680.257
690.472
70.123
700.373
710.0228
720.519
730.514
740.833
750.0382
760.0296
770.249
780.0733
790.719
80.34
800.0912
810.967
820.873
830.788
840.0774
850.592
860.341
870.21
880.291
890.356
90.33
900.0364
910.804
920.64
930.969
940.245
950.361
960.063
970.47
980.346
990.331



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: CNhs11181


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)
0002370 (thymus)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000307 (mouse neonate N2 sample)
0011280 (mouse thymus- neonate N02 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: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:1541-43F8&oldid=4578209"