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FF:10203-103F5: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:26, 29 March 2012


Name:tongue, adult
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sex28
ageM
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234267-50
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.0855
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.0492
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



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: CNhs12853

Jaspar motifP-value
MA0002.20.179
MA0003.10.129
MA0004.10.0302
MA0006.10.102
MA0007.10.43
MA0009.10.961
MA0014.10.903
MA0017.10.151
MA0018.20.00649
MA0019.10.0378
MA0024.10.0623
MA0025.10.464
MA0027.10.871
MA0028.14.53685e-6
MA0029.10.61
MA0030.10.968
MA0031.10.266
MA0035.20.0609
MA0038.10.013
MA0039.20.494
MA0040.10.95
MA0041.10.418
MA0042.10.75
MA0043.13.01681e-4
MA0046.10.00779
MA0047.20.708
MA0048.14.21031e-4
MA0050.12.68473e-4
MA0051.10.0112
MA0052.11.3823e-27
MA0055.10.00133
MA0057.10.2
MA0058.10.00257
MA0059.10.0266
MA0060.12.7766e-4
MA0061.10.0203
MA0062.21.51431e-11
MA0065.20.142
MA0066.10.691
MA0067.10.0455
MA0068.10.96
MA0069.10.852
MA0070.10.633
MA0071.10.872
MA0072.10.37
MA0073.10.817
MA0074.10.54
MA0076.15.62563e-7
MA0077.10.481
MA0078.10.402
MA0079.20.285
MA0080.21.19107e-4
MA0081.10.00905
MA0083.10.108
MA0084.10.626
MA0087.10.481
MA0088.10.308
MA0090.10.419
MA0091.10.0653
MA0092.10.367
MA0093.10.0212
MA0099.23.42099e-8
MA0100.10.0267
MA0101.10.00438
MA0102.20.0116
MA0103.10.00116
MA0104.20.00536
MA0105.10.186
MA0106.10.673
MA0107.10.00454
MA0108.22.79056e-19
MA0111.10.552
MA0112.23.44322e-4
MA0113.10.0139
MA0114.10.524
MA0115.10.0939
MA0116.10.772
MA0117.10.483
MA0119.10.495
MA0122.10.256
MA0124.10.776
MA0125.10.991
MA0131.10.0388
MA0135.10.203
MA0136.13.58086e-6
MA0137.20.255
MA0138.20.0937
MA0139.10.606
MA0140.10.0196
MA0141.10.0929
MA0142.10.456
MA0143.10.551
MA0144.10.75
MA0145.10.0189
MA0146.10.457
MA0147.10.00865
MA0148.10.902
MA0149.10.133
MA0150.10.027
MA0152.10.932
MA0153.10.879
MA0154.10.362
MA0155.10.151
MA0156.13.7369e-9
MA0157.10.414
MA0159.10.138
MA0160.10.359
MA0162.10.107
MA0163.10.381
MA0164.10.914
MA0258.10.0152
MA0259.10.0395



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: CNhs12853

Novel motifP-value
10.598
100.409
1000.421
1010.943
1020.521
1030.944
1040.686
1050.716
1060.0603
1070.028
1080.14
1090.775
110.68
1100.963
1110.528
1120.032
1130.992
1140.862
1150.00276
1160.206
1170.321
1180.143
1190.169
120.697
1200.528
1210.578
1220.293
1230.0258
1240.107
1250.738
1260.357
1270.465
1280.179
1290.858
130.773
1300.497
1310.505
1320.0962
1330.00976
1340.0629
1350.0197
1360.835
1370.19
1380.908
1390.155
140.694
1400.616
1410.48
1420.775
1430.0714
1440.715
1450.779
1460.483
1470.00772
1480.325
1490.0156
150.552
1500.568
1510.382
1520.084
1530.249
1540.707
1550.473
1560.0956
1570.917
1580.0919
1590.507
160.101
1600.303
1610.663
1620.794
1630.301
1640.282
1650.00929
1660.13
1670.208
1680.386
1690.0108
170.418
180.832
190.067
20.0108
200.0166
210.115
220.105
230.288
240.613
250.683
260.933
270.388
280.941
290.374
30.949
300.00353
310.554
320.0864
330.882
340.582
350.872
360.0166
370.38
380.634
390.177
40.666
400.461
410.524
420.467
430.951
444.3413e-4
450.0485
460.596
470.977
480.935
490.792
50.821
500.538
510.989
520.106
530.793
540.669
550.877
560.908
570.698
580.68
590.0829
60.961
600.123
610.672
620.498
630.211
640.981
650.267
660.0149
670.259
680.31
690.269
70.492
700.644
710.889
720.49
730.269
740.0479
750.976
760.0439
770.0183
780.178
790.169
80.459
800.792
810.0962
820.35
830.823
840.374
850.0245
860.419
870.693
880.631
890.0128
90.542
900.3
910.117
920.19
930.982
940.154
950.631
960.99
970.484
980.723
990.0701



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: CNhs12853


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
0000020 (sense organ)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000165 (mouth)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000930 (stomodeum)
0001007 (digestive system)
0001016 (nervous system)
0001032 (sensory system)
0001033 (gustatory system)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001555 (digestive tract)
0001723 (tongue)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0002539 (pharyngeal arch)
0004119 (endoderm-derived structure)
0004121 (ectoderm-derived structure)
0004362 (pharyngeal arch 1)
0004456 (entire sense organ system)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)
0008814 (pharyngeal arch system)
0008816 (embryonic head)

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

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