Personal tools

FF:822-18A4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 48: Line 48:
|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;822
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;822
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;822
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;822
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N20.CNhs11109.822-18A4.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N20.CNhs11109.822-18A4.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N20.CNhs11109.822-18A4.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/lung%252c%2520neonate%2520N20.CNhs11109.822-18A4.mm10.nobarcode.ctss.bed.gz

Revision as of 18:57, 4 August 2017


Name:lung, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11109
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuelung
dev stage20 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  SAMD00004879
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11109 CAGE DRX009041 DRR009915
Accession ID Mm9

Library idBAMCTSS
CNhs11109 DRZ001340 DRZ002723
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

CNhs11109

00
10
100.0659
1000
10000.059
10010.253
1002-0.0363
10030.193
10040
10050.2
10060.152
10070.0373
10080.0659
10090.441
101-0.0759
10100
1011-0.0788
10120.219
10130.0964
10140.0791
1015-0.223
10160.0534
10170.0659
10180.174
10190
1020
10200
1021-0.0487
10220.261
10230.0659
10240.598
10251.222
10260
10270
10280
10290.395
1030.113
10300.394
10310.279
10320.0744
1033-5.948308e-4
10340.0874
10350.0659
1036-0.0392
10370
10380.478
10390.163
1040
10400.514
10410.297



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: CNhs11109

Jaspar motifP-value
MA0002.20.359
MA0003.10.0686
MA0004.10.152
MA0006.10.0648
MA0007.10.794
MA0009.10.362
MA0014.10.667
MA0017.10.193
MA0018.27.88765e-5
MA0019.10.932
MA0024.11.16491e-4
MA0025.10.275
MA0027.10.611
MA0028.10.00215
MA0029.10.566
MA0030.10.166
MA0031.10.0139
MA0035.20.159
MA0038.10.313
MA0039.20.0059
MA0040.10.714
MA0041.10.23
MA0042.10.471
MA0043.10.0193
MA0046.12.87509e-9
MA0047.29.58928e-6
MA0048.10.523
MA0050.14.28818e-6
MA0051.10.00381
MA0052.10.0129
MA0055.10.349
MA0057.10.109
MA0058.10.0548
MA0059.10.0522
MA0060.11.10758e-12
MA0061.10.0755
MA0062.26.5658e-4
MA0065.20.739
MA0066.10.974
MA0067.10.528
MA0068.10.795
MA0069.10.471
MA0070.10.806
MA0071.10.323
MA0072.10.193
MA0073.10.864
MA0074.10.459
MA0076.14.38208e-4
MA0077.10.014
MA0078.10.00803
MA0079.20.154
MA0080.22.32115e-8
MA0081.10.294
MA0083.10.00386
MA0084.10.795
MA0087.10.63
MA0088.10.997
MA0090.10.0363
MA0091.10.867
MA0092.10.388
MA0093.10.124
MA0099.20.834
MA0100.10.144
MA0101.10.365
MA0102.20.287
MA0103.10.569
MA0104.20.00726
MA0105.10.151
MA0106.10.0273
MA0107.10.0308
MA0108.20.347
MA0111.10.178
MA0112.20.00934
MA0113.10.573
MA0114.10.0663
MA0115.10.0717
MA0116.10.136
MA0117.10.498
MA0119.10.0356
MA0122.10.202
MA0124.10.179
MA0125.10.0644
MA0131.10.113
MA0135.10.491
MA0136.10.0337
MA0137.20.712
MA0138.20.719
MA0139.10.109
MA0140.10.883
MA0141.10.134
MA0142.10.779
MA0143.10.262
MA0144.10.224
MA0145.10.00205
MA0146.10.518
MA0147.10.00803
MA0148.13.20513e-4
MA0149.10.271
MA0150.10.677
MA0152.10.369
MA0153.11.49493e-6
MA0154.10.00316
MA0155.10.257
MA0156.10.0272
MA0157.10.0117
MA0159.10.748
MA0160.10.168
MA0162.10.127
MA0163.10.634
MA0164.10.602
MA0258.10.171
MA0259.10.0193



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: CNhs11109

Novel motifP-value
10.544
100.999
1000.519
1010.404
1020.479
1030.141
1040.836
1050.389
1068.99126e-4
1070.00384
1080.969
1090.258
110.879
1100.678
1110.729
1120.227
1130.876
1140.386
1150.654
1160.956
1170.211
1180.893
1190.056
120.694
1200.314
1210.315
1220.681
1230.616
1240.418
1250.625
1260.205
1270.109
1280.00149
1290.1
130.0398
1300.012
1310.154
1320.395
1330.73
1340.937
1350.528
1360.256
1370.248
1380.0474
1390.469
140.248
1400.477
1410.152
1420.0556
1430.717
1440.966
1450.18
1460.813
1470.767
1480.47
1490.0434
150.325
1500.244
1510.146
1520.0451
1530.446
1540.32
1550.572
1560.0824
1570.812
1580.663
1590.0228
1600.0734
1610.897
1620.391
1630.885
1640.557
1650.688
1660.198
1670.604
1680.818
1690.00745
170.252
180.258
190.0371
20.163
200.306
210.599
220.128
230.0165
240.317
250.359
260.0662
270.743
280.458
290.529
30.481
300.749
310.819
320.703
330.912
340.53
350.311
360.849
370.0468
380.242
390.153
40.619
400.701
410.454
420.499
430.13
440.448
450.157
460.586
470.602
480.902
490.232
50.441
500.398
510.434
520.0639
530.299
540.483
550.985
560.295
570.657
580.539
590.095
60.926
600.0413
610.869
620.509
630.154
640.72
650.142
660.0715
670.358
680.669
690.794
70.306
700.234
710.264
720.93
730.194
740.799
750.807
760.502
770.185
780.882
790.799
80.983
800.854
810.929
820.234
830.313
840.378
850.0325
860.885
870.0219
880.739
890.309
90.159
900.908
910.336
920.0722
930.444
940.853
950.685
960.378
970.66
980.856
990.24



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: CNhs11109


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)
0002048 (lung)
0002100 (trunk)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000308 (mouse neonate N20 sample)
0011428 (mouse lung- neonate N20 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:0001041 (foregut)
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
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:822-18A4&oldid=4342896"