Personal tools

FF:1352-25E3: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 46: Line 46:
|library_id=CNhs11121
|library_id=CNhs11121
|library_id_phase_based=2:CNhs11121
|library_id_phase_based=2:CNhs11121
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N25.CNhs11121.1352-25E3.mm9.nobarcode.rdna.fa.gz
|name=intestine, neonate N25
|name=intestine, neonate N25
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 17:48, 17 May 2017


Name:intestine, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11121
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
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  SAMD00004971
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11121 CAGE DRX009002 DRR009876
Accession ID Mm9

Library idBAMCTSS
CNhs11121 DRZ001301 DRZ002684
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

CNhs11121

00
10
100
1000
10000.114
10010.0979
10020.125
1003-0.0856
10040
10050.215
10060
1007-0.0276
10082.076
10090.027
101-0.109
10100
1011-0.118
10120.0582
10130.266
1014-0.00956
1015-0.256
1016-0.323
10170
10180.4
10190
1020
10200
1021-0.0487
10220.0156
10230
1024-0.00489
10250.619
10260
1027-0.00439
10280
10290.612
1030.085
10300.085
1031-0.12
10320.612
1033-0.0752
10340.223
10350
1036-0.0979
10370
10380.0291
10390.0997
1040.361
1040-0.222
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: CNhs11121

Jaspar motifP-value
MA0002.20.0622
MA0003.10.284
MA0004.10.587
MA0006.10.0566
MA0007.10.823
MA0009.10.316
MA0014.10.311
MA0017.14.25992e-20
MA0018.20.0187
MA0019.10.374
MA0024.10.0361
MA0025.10.243
MA0027.10.989
MA0028.10.758
MA0029.10.886
MA0030.10.84
MA0031.10.5
MA0035.20.00171
MA0038.10.589
MA0039.20.00362
MA0040.10.176
MA0041.10.249
MA0042.10.774
MA0043.10.084
MA0046.14.67169e-32
MA0047.20.0018
MA0048.10.473
MA0050.12.28517e-7
MA0051.13.30636e-5
MA0052.15.76546e-5
MA0055.10.304
MA0057.10.162
MA0058.10.416
MA0059.10.943
MA0060.10.0083
MA0061.10.294
MA0062.20.711
MA0065.22.63168e-12
MA0066.10.131
MA0067.10.192
MA0068.10.0948
MA0069.10.182
MA0070.10.0449
MA0071.10.297
MA0072.10.63
MA0073.10.824
MA0074.10.274
MA0076.10.302
MA0077.10.297
MA0078.10.31
MA0079.20.142
MA0080.20.00117
MA0081.10.331
MA0083.10.787
MA0084.10.675
MA0087.10.935
MA0088.10.747
MA0090.10.974
MA0091.10.773
MA0092.10.477
MA0093.10.535
MA0099.20.00766
MA0100.10.175
MA0101.10.901
MA0102.20.18
MA0103.13.02485e-5
MA0104.20.0813
MA0105.10.0639
MA0106.10.201
MA0107.10.982
MA0108.20.626
MA0111.10.877
MA0112.29.72318e-6
MA0113.10.937
MA0114.11.48986e-26
MA0115.11.11528e-10
MA0116.10.173
MA0117.10.865
MA0119.10.0219
MA0122.10.606
MA0124.10.45
MA0125.10.153
MA0131.10.476
MA0135.10.374
MA0136.10.00307
MA0137.20.988
MA0138.20.428
MA0139.10.0661
MA0140.10.163
MA0141.16.8322e-5
MA0142.10.173
MA0143.10.167
MA0144.10.147
MA0145.10.0039
MA0146.10.308
MA0147.10.141
MA0148.13.92859e-4
MA0149.10.0369
MA0150.10.52
MA0152.10.171
MA0153.15.05642e-29
MA0154.10.0316
MA0155.10.542
MA0156.10.0723
MA0157.10.993
MA0159.10.0049
MA0160.10.00934
MA0162.10.272
MA0163.10.0831
MA0164.10.997
MA0258.10.0097
MA0259.10.241



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: CNhs11121

Novel motifP-value
10.1
100.131
1000.846
1010.934
1020.893
1030.16
1040.858
1050.459
1060.0111
1070.0246
1080.923
1090.0611
110.179
1100.199
1110.0565
1120.0202
1130.415
1140.0495
1150.62
1160.361
1170.267
1180.516
1190.175
120.941
1200.515
1210.789
1220.879
1230.245
1240.934
1250.484
1260.0871
1270.455
1280.0399
1290.337
139.72606e-4
1300.932
1310.0692
1320.695
1330.881
1340.833
1350.303
1360.37
1370.794
1380.612
1390.0459
140.725
1400.112
1410.22
1420.734
1430.205
1440.649
1450.153
1460.376
1470.237
1480.179
1490.626
150.167
1500.348
1510.364
1520.0578
1530.61
1540.304
1550.541
1560.491
1570.85
1580.563
1590.164
1600.187
1610.624
1620.783
1630.451
1640.106
1650.476
1660.995
1670.734
1680.77
1690.00378
170.0476
180.113
190.048
20.37
200.851
210.886
220.328
230.285
240.758
250.735
260.00271
270.712
280.45
290.245
30.206
300.531
310.732
320.0283
330.233
340.821
350.683
360.78
370.0234
380.362
390.129
40.635
400.436
410.502
420.481
430.222
440.226
450.43
460.168
470.321
480.294
490.138
50.409
500.48
510.615
520.0792
530.89
540.525
550.583
560.384
570.768
580.293
590.275
60.659
600.0459
610.157
620.277
630.168
640.725
650.213
660.374
670.459
680.158
690.628
70.0622
700.0781
710.0857
720.596
730.109
740.934
750.106
760.914
770.169
780.0467
790.919
80.181
800.782
810.663
820.124
830.266
840.494
850.0309
860.226
870.878
880.592
890.352
90.725
900.159
910.28
920.355
930.671
940.872
950.144
960.772
970.875
980.854
990.0829



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: CNhs11121


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)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal 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)
0011480 (mouse intestine- 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: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:1352-25E3&oldid=4335634"