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{{f5samples
{{f5samples
|F5samples=
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|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101610
|fonse_cell_line=FF:0101610
|fonse_cell_line_closure=FF:0101610
|fonse_cell_line_closure=FF:0101610

Revision as of 16:58, 29 March 2012


Name:thyroid carcinoma cell line:TCO-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuethyroid
dev stageNA
sexmale
ageunknown
cell typeunclassifiable
cell lineTCO-1
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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-penis0.271
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-lymphoma0.392
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11872

Jaspar motifP-value
MA0002.29.93538e-4
MA0003.10.138
MA0004.10.661
MA0006.10.748
MA0007.10.417
MA0009.10.895
MA0014.10.784
MA0017.10.0215
MA0018.20.396
MA0019.10.689
MA0024.10.00117
MA0025.10.216
MA0027.10.235
MA0028.12.47809e-7
MA0029.10.701
MA0030.10.958
MA0031.10.673
MA0035.20.186
MA0038.10.0597
MA0039.20.574
MA0040.10.849
MA0041.10.827
MA0042.10.967
MA0043.10.451
MA0046.10.0358
MA0047.20.618
MA0048.10.111
MA0050.10.846
MA0051.10.31
MA0052.10.333
MA0055.10.0215
MA0057.10.362
MA0058.10.937
MA0059.10.839
MA0060.12.84936e-6
MA0061.10.00456
MA0062.22.90865e-9
MA0065.20.0169
MA0066.10.209
MA0067.10.264
MA0068.10.218
MA0069.10.795
MA0070.10.917
MA0071.10.0726
MA0072.10.12
MA0073.10.918
MA0074.10.773
MA0076.13.8317e-8
MA0077.10.99
MA0078.10.22
MA0079.20.767
MA0080.25.59751e-8
MA0081.10.745
MA0083.10.611
MA0084.10.966
MA0087.10.0973
MA0088.10.122
MA0090.10.102
MA0091.10.0025
MA0092.10.243
MA0093.10.557
MA0099.20.999
MA0100.10.568
MA0101.10.166
MA0102.20.00511
MA0103.10.0841
MA0104.20.633
MA0105.12.73792e-4
MA0106.10.84
MA0107.10.0551
MA0108.20.0797
MA0111.10.548
MA0112.26.94729e-4
MA0113.10.21
MA0114.10.0773
MA0115.10.755
MA0116.10.00249
MA0117.10.283
MA0119.10.982
MA0122.10.772
MA0124.10.2
MA0125.10.677
MA0131.10.108
MA0135.10.129
MA0136.10.0377
MA0137.20.652
MA0138.20.223
MA0139.10.868
MA0140.10.654
MA0141.10.174
MA0142.10.0564
MA0143.10.0115
MA0144.10.444
MA0145.10.094
MA0146.10.0227
MA0147.10.61
MA0148.10.46
MA0149.10.103
MA0150.10.0596
MA0152.10.48
MA0153.10.193
MA0154.10.00152
MA0155.10.0819
MA0156.10.0679
MA0157.10.925
MA0159.10.143
MA0160.10.0628
MA0162.10.73
MA0163.11.87462e-4
MA0164.10.279
MA0258.10.00646
MA0259.10.202



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: CNhs11872

Novel motifP-value
10.249
100.671
1000.41
1010.678
1020.959
1030.084
1040.941
1050.0701
1060.0413
1070.117
1080.859
1090.682
110.159
1100.575
1110.12
1120.0358
1130.12
1140.0182
1150.79
1160.592
1170.446
1180.641
1190.0959
120.963
1200.637
1210.939
1220.73
1230.378
1240.0199
1250.903
1260.718
1270.638
1280.00225
1290.023
130.765
1300.0744
1310.533
1320.774
1330.214
1340.177
1350.111
1360.116
1370.168
1380.522
1398.94489e-5
140.361
1400.165
1410.0577
1420.0521
1430.103
1440.875
1450.311
1460.406
1470.989
1480.0654
1490.0589
150.143
1500.826
1510.294
1520.477
1530.634
1540.549
1550.334
1560.22
1570.173
1580.0519
1590.201
160.28
1600.811
1610.701
1620.922
1630.386
1640.661
1650.49
1660.806
1670.719
1680.712
1690.0199
170.118
180.14
190.104
20.212
200.217
210.359
220.151
230.0152
240.826
250.47
260.707
270.101
280.865
290.699
30.291
300.937
310.497
320.262
330.411
340.128
350.0752
360.836
370.208
380.378
390.867
40.698
400.795
410.0173
420.637
430.0874
440.378
450.251
460.128
470.282
480.609
490.0917
50.0473
500.893
510.248
520.11
530.62
540.271
550.248
560.281
570.574
580.287
590.0463
60.813
600.0861
610.753
620.0927
630.409
640.544
650.0552
660.063
670.979
680.56
690.482
70.303
700.336
710.23
720.28
730.505
740.568
750.196
760.462
770.197
780.384
790.209
80.556
800.0318
810.245
820.0178
830.53
840.5
850.0122
860.23
870.766
880.98
890.0399
90.181
900.177
910.347
920.0107
930.0588
940.138
950.533
960.127
970.724
980.528
990.44



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: CNhs11872


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
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002046 (thyroid gland)
0002050 (embryonic structure)
0002368 (endocrine gland)
0002530 (gland)
0002532 (epiblast (generic))
0003091 (thyroid primordium)
0003104 (mesenchyme)
0004117 (pharyngeal pouch)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006562 (pharynx)
0007026 (primitive gut)
0007123 (pharyngeal pouch 2)
0007689 (thyroid diverticulum)
0007690 (early pharyngeal endoderm)
0008814 (pharyngeal arch system)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

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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