Personal tools

FF:32-1B4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000005,UBERON:0000020,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000073,UBERON:0000153,UBERON:0000165,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000925,UBERON:0000930,UBERON:0001007,UBERON:0001016,UBERON:0001032,UBERON:0001033,UBERON:0001062,UBERON:0001444,UBERON:0001555,UBERON:0001723,UBERON:0002050,UBERON:0002532,UBERON:0002539,UBERON:0003212,UBERON:0004119,UBERON:0004121,UBERON:0004362,UBERON:0004456,UBERON:0005423,UBERON:0005726,UBERON:0006260,UBERON:0006756,UBERON:0006757,UBERON:0007023,UBERON:0007026,UBERON:0008814,UBERON:0008816
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000922,UBERON:0001723,UBERON:0006562,UBERON:0000033,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0004121,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004921,UBERON:0000161,UBERON:0005423,UBERON:0001444,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0003103,UBERON:0005291,UBERON:0003102,UBERON:0000020,UBERON:0000078,UBERON:0000072,UBERON:0003104,UBERON:0001032,UBERON:0000925,UBERON:0006598,UBERON:0004185,UBERON:0002532,UBERON:0001555,UBERON:0000065,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0000165,UBERON:0007026,UBERON:0001041,UBERON:0004456,UBERON:0000166,UBERON:0001557,UBERON:0001033,UBERON:0001042,UBERON:0008814,UBERON:0009142,UBERON:0000930,UBERON:0006601,UBERON:0006595,UBERON:0006603,UBERON:0009145,UBERON:0010056
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=

Revision as of 18:20, 8 June 2012


Name:tongue, adult
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuetongue
dev stageadult
sexmale
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
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

CNhs10499

00
10
100
1000
10001.018
10010.493
10020
10030.306
10040
10050.0234
10060.587
1007-0.113
10080
10090.0804
101-0.00874
10100
10110.0752
10120
1013-0.0329
10140
1015-0.155
1016-0.181
10170.725
10180.571
10190
1020
10200
10210
10220.866
10230
10240.343
10250
10260
10270
10280
1029-0.0136
103-0.061
10300
1031-0.352
10320.101
10330.0887
10340.0887
10350.0887
1036-0.106
10370
1038-0.0729
10390.395
1040
10400.0569
10410.162



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 no result for this sample


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: CNhs10499

Jaspar motifP-value
MA0002.20.227
MA0003.10.203
MA0004.10.635
MA0006.10.148
MA0007.10.656
MA0009.10.311
MA0014.10.519
MA0017.10.0575
MA0018.20.12
MA0019.10.864
MA0024.17.56137e-5
MA0025.10.138
MA0027.10.386
MA0028.10.00515
MA0029.10.541
MA0030.10.0104
MA0031.10.032
MA0035.20.00797
MA0038.10.283
MA0039.20.00598
MA0040.10.144
MA0041.10.95
MA0042.10.559
MA0043.10.117
MA0046.11.07965e-13
MA0047.20.0125
MA0048.10.0203
MA0050.10.184
MA0051.10.794
MA0052.15.20507e-50
MA0055.10.0179
MA0057.10.0466
MA0058.10.425
MA0059.10.112
MA0060.11.05901e-5
MA0061.10.65
MA0062.26.70067e-6
MA0065.20.12
MA0066.10.371
MA0067.10.991
MA0068.10.338
MA0069.10.422
MA0070.10.862
MA0071.10.728
MA0072.10.467
MA0073.10.304
MA0074.10.311
MA0076.10.00107
MA0077.10.16
MA0078.10.41
MA0079.20.0205
MA0080.20.00114
MA0081.10.0416
MA0083.10.00397
MA0084.10.725
MA0087.10.567
MA0088.10.983
MA0090.10.0288
MA0091.10.668
MA0092.10.34
MA0093.10.595
MA0099.22.16612e-15
MA0100.10.0282
MA0101.10.389
MA0102.20.333
MA0103.10.0118
MA0104.20.182
MA0105.10.578
MA0106.10.156
MA0107.10.606
MA0108.24.02479e-21
MA0111.10.817
MA0112.20.00183
MA0113.10.838
MA0114.10.267
MA0115.10.00534
MA0116.10.903
MA0117.10.865
MA0119.10.524
MA0122.10.348
MA0124.10.78
MA0125.10.377
MA0131.10.219
MA0135.10.199
MA0136.14.71533e-5
MA0137.20.827
MA0138.21.76694e-4
MA0139.10.986
MA0140.10.0293
MA0141.10.0399
MA0142.10.154
MA0143.10.206
MA0144.10.409
MA0145.10.0073
MA0146.10.335
MA0147.10.218
MA0148.10.0433
MA0149.10.643
MA0150.10.00658
MA0152.10.998
MA0153.12.13702e-9
MA0154.10.0601
MA0155.10.668
MA0156.16.89293e-4
MA0157.10.0249
MA0159.10.103
MA0160.10.057
MA0162.10.537
MA0163.10.943
MA0164.10.369
MA0258.10.00985
MA0259.10.166



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: CNhs10499

Novel motifP-value
10.365
100.845
1000.816
1010.368
1020.556
1030.591
1040.947
1050.133
1060.0457
1070.103
1080.741
1090.372
110.739
1100.624
1110.13
1120.785
1130.666
1140.222
1150.148
1160.251
1170.495
1180.199
1190.0126
120.625
1200.625
1210.202
1220.346
1230.63
1240.354
1250.479
1260.439
1270.213
1280.125
1290.472
130.0237
1300.874
1310.386
1320.832
1330.968
1340.867
1350.982
1360.167
1370.82
1380.847
1390.0595
140.119
1400.0975
1410.132
1420.579
1430.173
1440.775
1450.613
1460.755
1470.882
1480.554
1490.173
150.82
1500.54
1510.182
1520.0265
1530.571
1540.926
1550.0845
1560.559
1570.0887
1580.773
1590.342
1600.412
1610.11
1620.329
1630.764
1640.708
1650.127
1660.691
1670.0245
1680.128
1690.00537
170.0326
180.695
190.0967
20.258
200.329
210.679
220.165
230.123
240.33
250.851
260.174
270.689
280.615
290.695
30.63
300.1
310.709
320.825
330.742
340.483
350.348
360.0491
370.0692
380.736
390.333
40.641
400.484
410.154
420.735
430.469
440.829
450.185
460.304
470.698
480.702
490.682
50.624
500.438
510.687
520.183
530.419
540.235
550.946
560.326
570.766
580.466
590.156
60.805
600.0791
610.588
620.357
630.0694
640.92
650.411
660.956
670.238
680.321
690.283
70.242
700.0428
710.218
720.778
730.0416
740.842
750.778
760.0402
770.0246
780.214
790.899
80.821
800.974
810.0855
820.193
830.611
840.0595
850.00828
860.218
870.151
880.824
890.117
90.269
900.675
910.575
920.327
930.329
940.553
950.54
960.162
970.479
980.849
990.417



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: CNhs10499


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)
0007023 (adult organism)
0000922 (embryo)
0001723 (tongue)
0006562 (pharynx)
0000033 (head)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0004921 (subdivision of digestive tract)
0000161 (orifice)
0005423 (developing anatomical structure)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0003103 (compound organ)
0005291 (embryonic tissue)
0003102 (surface structure)
0000020 (sense organ)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000072 (segment of respiratory tract)
0003104 (mesenchyme)
0001032 (sensory system)
0000925 (endoderm)
0006598 (presumptive structure)
0004185 (endodermal part of digestive tract)
0002532 (epiblast (generic))
0001555 (digestive tract)
0000065 (respiratory tract)
0001004 (respiratory system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000924 (ectoderm)
0000165 (mouth)
0007026 (primitive gut)
0001041 (foregut)
0004456 (entire sense organ system)
0000166 (oral opening)
0001557 (upper respiratory tract)
0001033 (gustatory system)
0001042 (chordate pharynx)
0008814 (pharyngeal arch system)
0009142 (entire embryonic mesenchyme)
0000930 (stomodeum)
0006601 (presumptive ectoderm)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0009145 (pharyngeal region of foregut)
0010056 (future tongue)

FF: FANTOM5
NA

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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:32-1B4&oldid=1831757"