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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100400,FF:0100453
|fonse_cell_line=FF:0100400,FF:0100453
|fonse_cell_line_closure=FF:0100400,FF:0100453
|fonse_cell_line_closure=FF:0100400,FF:0100453

Revision as of 16:57, 29 March 2012


Name:fibrosarcoma cell line:HT-1080
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepelvis
dev stageNA
sexmale
age35
cell typeunclassifiable
cell lineHT-1080
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-penis0.335
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-lymphoma0.411
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11860

Jaspar motifP-value
MA0002.20.96
MA0003.10.246
MA0004.10.18
MA0006.10.815
MA0007.10.762
MA0009.10.375
MA0014.10.424
MA0017.10.302
MA0018.20.0297
MA0019.10.0325
MA0024.10.00382
MA0025.10.3
MA0027.10.635
MA0028.14.51543e-12
MA0029.10.893
MA0030.10.356
MA0031.10.295
MA0035.20.661
MA0038.10.182
MA0039.20.0211
MA0040.10.478
MA0041.10.123
MA0042.10.521
MA0043.10.00212
MA0046.10.00872
MA0047.20.508
MA0048.11.64951e-4
MA0050.10.3
MA0051.10.855
MA0052.10.0155
MA0055.10.019
MA0057.10.899
MA0058.10.623
MA0059.10.0216
MA0060.10.61
MA0061.10.0824
MA0062.22.53062e-13
MA0065.20.138
MA0066.10.312
MA0067.10.0132
MA0068.10.758
MA0069.10.419
MA0070.10.629
MA0071.10.671
MA0072.10.535
MA0073.10.868
MA0074.10.558
MA0076.16.77442e-14
MA0077.10.472
MA0078.10.915
MA0079.20.196
MA0080.20.0702
MA0081.10.501
MA0083.10.753
MA0084.10.34
MA0087.10.144
MA0088.17.28038e-4
MA0090.10.0521
MA0091.10.0847
MA0092.10.395
MA0093.10.156
MA0099.21.36613e-11
MA0100.10.381
MA0101.10.815
MA0102.20.02
MA0103.10.344
MA0104.20.0237
MA0105.10.435
MA0106.10.0277
MA0107.10.161
MA0108.21.92539e-9
MA0111.10.718
MA0112.20.00845
MA0113.10.128
MA0114.10.127
MA0115.10.792
MA0116.10.347
MA0117.10.391
MA0119.10.413
MA0122.10.347
MA0124.10.423
MA0125.10.272
MA0131.10.101
MA0135.16.85925e-4
MA0136.10.509
MA0137.20.212
MA0138.20.341
MA0139.10.233
MA0140.10.677
MA0141.10.933
MA0142.10.191
MA0143.10.594
MA0144.10.39
MA0145.10.141
MA0146.10.106
MA0147.10.00159
MA0148.10.962
MA0149.10.0473
MA0150.10.112
MA0152.10.669
MA0153.10.0109
MA0154.10.017
MA0155.10.0157
MA0156.12.96078e-5
MA0157.10.977
MA0159.10.314
MA0160.10.306
MA0162.10.733
MA0163.10.344
MA0164.10.0994
MA0258.10.0692
MA0259.10.178



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: CNhs11860

Novel motifP-value
10.118
100.358
1000.783
1010.463
1020.294
1030.498
1040.675
1050.254
1060.41
1070.11
1080.155
1090.334
110.293
1100.344
1110.0135
1120.544
1130.235
1140.649
1150.923
1160.604
1170.934
1180.578
1190.436
120.57
1200.182
1210.773
1220.81
1230.0128
1240.735
1250.184
1261
1270.104
1280.612
1290.69
130.901
1300.384
1310.149
1320.748
1330.359
1340.717
1350.111
1360.0611
1370.242
1380.274
1390.849
140.331
1400.821
1410.833
1420.694
1430.128
1440.915
1450.544
1460.588
1470.589
1480.413
1490.474
150.266
1500.35
1510.84
1520.966
1530.902
1540.403
1550.0967
1560.663
1570.795
1580.154
1590.0779
160.827
1600.824
1610.654
1620.621
1630.528
1640.0125
1650.98
1660.754
1670.0552
1680.798
1690.286
170.899
180.13
190.418
20.819
200.277
210.151
220.246
230.0907
240.688
250.435
260.5
270.288
280.302
290.113
30.307
300.125
310.975
320.0706
330.878
340.187
350.446
360.592
370.917
380.975
390.518
40.926
400.256
410.512
420.33
430.411
440.675
450.318
460.287
470.496
480.208
490.519
50.5
500.957
510.612
520.0216
530.575
540.808
550.706
560.941
570.0591
580.442
590.329
60.507
600.257
610.301
620.741
630.771
640.549
650.907
660.00107
670.357
680.15
690.474
70.526
700.551
710.626
720.364
730.556
740.634
750.748
760.903
770.987
780.633
790.464
80.115
800.0335
810.628
820.148
830.425
840.835
850.0183
860.711
870.2
880.139
890.386
90.144
900.362
910.174
920.635
930.525
940.514
950.233
960.898
970.523
980.897
990.072



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: CNhs11860


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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