Personal tools

FF:1350-25C3: 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;1350
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1350
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1350
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1350
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520neonate%2520N20.CNhs11195.1350-25C3.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520neonate%2520N20.CNhs11195.1350-25C3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520neonate%2520N20.CNhs11195.1350-25C3.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/bone%2520%2528os%2520femoris%2529%252c%2520neonate%2520N20.CNhs11195.1350-25C3.mm10.nobarcode.ctss.bed.gz

Revision as of 18:13, 4 August 2017


Name:bone (os femoris), neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11195
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuebone (os femoris)
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  SAMD00004931
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11195 CAGE DRX008939 DRR009813
Accession ID Mm9

Library idBAMCTSS
CNhs11195 DRZ001238 DRZ002621
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

CNhs11195

00
10
100
1000
10000.535
10010.304
1002-0.0587
10030.116
10040
10050.172
10060.368
10070.0791
10080
10090.2
1010.00531
10100
10110
10120
1013-0.118
10140.207
1015-0.182
1016-0.072
10170
10180
10190
1020
10200
10210.172
10220.522
10230
10240.172
10250
10260
10270
10280
10290.0728
1031.192
10300.39
10310.0306
10320.0115
10330.00808
10340
10350.172
10360.163
10370
1038-0.113
10390.0859
1040
10400.0576
10410.172



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: CNhs11195

Jaspar motifP-value
MA0002.20.00741
MA0003.10.0732
MA0004.10.323
MA0006.10.0902
MA0007.10.668
MA0009.10.443
MA0014.10.744
MA0017.10.792
MA0018.24.83997e-4
MA0019.10.247
MA0024.10.19
MA0025.10.121
MA0027.10.0906
MA0028.10.0682
MA0029.10.571
MA0030.10.566
MA0031.10.456
MA0035.20.426
MA0038.10.0424
MA0039.20.591
MA0040.10.498
MA0041.10.106
MA0042.10.592
MA0043.10.00939
MA0046.11.95212e-6
MA0047.20.438
MA0048.10.92
MA0050.10.647
MA0051.10.803
MA0052.11.27095e-5
MA0055.10.326
MA0057.10.334
MA0058.10.22
MA0059.10.464
MA0060.10.0589
MA0061.10.107
MA0062.20.0166
MA0065.20.18
MA0066.10.235
MA0067.10.184
MA0068.10.422
MA0069.10.331
MA0070.10.665
MA0071.10.885
MA0072.10.75
MA0073.10.806
MA0074.10.979
MA0076.10.0169
MA0077.10.43
MA0078.10.323
MA0079.20.0676
MA0080.20.00702
MA0081.10.426
MA0083.10.0988
MA0084.10.814
MA0087.10.477
MA0088.10.752
MA0090.10.717
MA0091.10.151
MA0092.10.521
MA0093.10.268
MA0099.20.702
MA0100.10.732
MA0101.10.901
MA0102.20.791
MA0103.10.0102
MA0104.20.152
MA0105.10.00169
MA0106.10.435
MA0107.10.815
MA0108.20.493
MA0111.10.648
MA0112.21.84616e-7
MA0113.10.883
MA0114.10.391
MA0115.10.302
MA0116.10.00488
MA0117.10.874
MA0119.10.106
MA0122.10.707
MA0124.10.929
MA0125.10.355
MA0131.10.931
MA0135.10.0936
MA0136.10.896
MA0137.20.0406
MA0138.20.846
MA0139.10.832
MA0140.19.46226e-9
MA0141.10.0762
MA0142.10.904
MA0143.10.371
MA0144.10.49
MA0145.10.229
MA0146.10.644
MA0147.10.308
MA0148.10.503
MA0149.10.342
MA0150.10.232
MA0152.10.0214
MA0153.11.58027e-6
MA0154.10.00411
MA0155.10.503
MA0156.10.819
MA0157.10.706
MA0159.10.15
MA0160.10.6
MA0162.10.149
MA0163.12.12311e-5
MA0164.10.961
MA0258.18.20917e-4
MA0259.10.852



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: CNhs11195

Novel motifP-value
10.0937
100.0733
1000.537
1010.871
1020.891
1030.167
1040.627
1050.288
1060.0854
1070.115
1080.905
1090.0794
110.223
1100.197
1110.349
1120.381
1130.909
1140.388
1150.931
1160.446
1170.117
1180.399
1190.804
120.841
1200.519
1210.895
1220.893
1230.534
1240.195
1250.394
1260.374
1270.137
1280.164
1290.827
130.0137
1300.608
1310.713
1320.539
1330.772
1340.874
1350.78
1360.195
1370.4
1380.566
1390.765
140.876
1400.18
1410.335
1420.757
1430.174
1440.15
1450.363
1460.903
1470.993
1480.416
1490.92
150.418
1500.408
1510.202
1520.271
1530.975
1540.864
1550.651
1560
1570.629
1580.724
1590.381
1600.0752
1610.766
1620.754
1630.455
1640.24
1650.742
1660.957
1670.411
1680.844
1690.00298
170.268
180.785
190.041
20.606
200.268
210.5
220.454
230.646
240.816
250.507
260.0073
270.75
280.512
290.22
30.0849
300.636
310.425
320.00169
330.961
340.365
350.709
360.878
370.0661
380.0662
390.616
40.856
400.686
410.937
420.361
430.184
440.619
450.651
460.0635
470.373
480.544
490.33
56.92008e-5
500.281
510.733
520.286
530.68
540.675
550.912
560.297
570.531
580.768
590.0142
60.672
600.143
610.708
620.279
630.203
640.699
650.17
660.515
670.123
680.649
690.584
70.0859
700.359
710.0156
720.959
730.219
740.899
750.213
760.764
770.737
780.015
790.87
80.155
800.328
810.411
820.562
830.594
840.371
850.0366
860.766
870.131
880.39
890.551
90.464
900.958
910.231
920.311
930.792
940.453
950.393
960.745
970.706
980.681
990.658



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: CNhs11195


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)
0000981 (femur)
0001474 (bone element)
0000479 (tissue)
0011216 (organ system subdivision)
0000062 (organ)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0002472 (stylopod)
0008784 (lower limb segment)
0001062 (anatomical entity)
0000480 (anatomical group)
0006058 (multi-limb segment region)
0003608 (hindlimb long bone)
0003826 (upper leg bone)
0008202 (bone of hip region)
0000075 (subdivision of skeletal system)
0004381 (skeleton of limb)
0007273 (pelvic appendage skeleton)
0004765 (skeletal element)
0010912 (subdivision of skeleton)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0002513 (endochondral bone)
0004375 (bone of free limb or fin)
0010740 (bone of appendage girdle complex)
0002529 (limb segment)
0010363 (endochondral element)
0010538 (paired limb/fin segment)
0002428 (limb bone)
0010742 (bone of pelvic complex)
0002495 (long bone)
0003464 (hindlimb bone)
0003606 (limb long bone)
0005893 (leg bone)
0010317 (germ layer / neural crest derived structure)
0010712 (limb skeleton subdivision)
0010758 (subdivision of organism along appendicular axis)
0010707 (appendage girdle complex)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0000978 (leg)
0002103 (hindlimb)
0000376 (hindlimb stylopod)
0001441 (hindlimb skeleton)
0011249 (appendicular skeletal system)
0000154 (posterior region of body)
0010709 (pelvic complex)
0002091 (appendicular skeleton)
0004288 (skeleton)

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)
0011467 (mouse bone- os femoris - 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:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0003104 (mesenchyme)
UBERON:0005866 (pre-cartilage condensation)
UBERON:0006234 (femur pre-cartilage condensation)
UBERON:0010316 (germ layer / neural crest)
UBERON:0010882 (limb bone pre-cartilage condensation)
UBERON:0010886 (hindlimb bone pre-cartilage condensation)
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1350-25C3&oldid=4342209"