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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:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100400,FF:0101120
|fonse_cell_line=FF:0100400,FF:0101120
|fonse_cell_line_closure=FF:0100400,FF:0101120
|fonse_cell_line_closure=FF:0100400,FF:0101120

Revision as of 16:50, 29 March 2012


Name:carcinosarcoma cell line:JHUCS-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueuterus
dev stageNA
sexfemale
age56
cell typeunclassifiable
cell lineJHUCS-1
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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-Neural0.0481
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-penis0.298
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-lymphoma0.572
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11747

Jaspar motifP-value
MA0002.21.84688e-6
MA0003.10.127
MA0004.10.968
MA0006.10.284
MA0007.10.594
MA0009.10.604
MA0014.10.794
MA0017.10.0105
MA0018.20.324
MA0019.10.492
MA0024.11.84184e-6
MA0025.10.956
MA0027.10.596
MA0028.10.406
MA0029.10.995
MA0030.10.211
MA0031.10.025
MA0035.20.142
MA0038.10.00301
MA0039.20.365
MA0040.10.183
MA0041.10.331
MA0042.10.422
MA0043.10.718
MA0046.10.0784
MA0047.20.00276
MA0048.10.497
MA0050.11.00426e-4
MA0051.10.0269
MA0052.10.00777
MA0055.10.747
MA0057.10.224
MA0058.10.874
MA0059.10.494
MA0060.19.63325e-9
MA0061.10.0121
MA0062.20.929
MA0065.20.00224
MA0066.10.0352
MA0067.10.92
MA0068.10.932
MA0069.10.944
MA0070.10.0415
MA0071.10.551
MA0072.10.528
MA0073.10.559
MA0074.10.184
MA0076.10.119
MA0077.10.273
MA0078.10.527
MA0079.20.665
MA0080.27.176e-14
MA0081.10.0522
MA0083.10.0631
MA0084.10.337
MA0087.10.124
MA0088.10.815
MA0090.10.0137
MA0091.10.613
MA0092.10.199
MA0093.10.933
MA0099.27.05528e-21
MA0100.10.221
MA0101.10.0714
MA0102.20.01
MA0103.10.256
MA0104.20.682
MA0105.10.00576
MA0106.10.15
MA0107.10.0227
MA0108.20.111
MA0111.10.584
MA0112.27.71818e-5
MA0113.10.0715
MA0114.10.0377
MA0115.10.529
MA0116.10.0122
MA0117.10.815
MA0119.10.0744
MA0122.10.182
MA0124.10.383
MA0125.10.788
MA0131.10.399
MA0135.10.286
MA0136.14.75598e-13
MA0137.20.00888
MA0138.20.94
MA0139.10.0591
MA0140.10.0582
MA0141.10.0466
MA0142.10.578
MA0143.10.438
MA0144.10.00303
MA0145.10.0601
MA0146.10.103
MA0147.10.912
MA0148.10.01
MA0149.10.0213
MA0150.17.92747e-5
MA0152.10.983
MA0153.10.209
MA0154.10.00684
MA0155.10.306
MA0156.11.8093e-5
MA0157.10.0134
MA0159.10.0109
MA0160.10.0869
MA0162.10.227
MA0163.19.09081e-5
MA0164.10.773
MA0258.10.00827
MA0259.10.629



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: CNhs11747

Novel motifP-value
10.202
100.188
1000.951
1010.889
1020.592
1030.066
1040.357
1050.148
1060.0137
1070.125
1080.593
1090.0314
110.0996
1100.386
1110.833
1120.0482
1130.36
1140.0151
1150.824
1160.626
1170.164
1180.431
1190.167
120.321
1200.309
1210.905
1220.75
1230.695
1240.733
1250.912
1260.172
1270.102
1280.0549
1290.2
130.313
1300.652
1310.277
1320.9
1330.265
1340.62
1350.0691
1360.859
1370.191
1380.334
1390.046
140.529
1400.76
1410.5
1420.557
1430.00381
1440.943
1450.282
1460.785
1470.773
1480.0324
1490.0248
150.169
1500.549
1510.375
1520.0253
1530.799
1540.912
1550.832
1560.784
1570.654
1580.941
1590.017
160.204
1600.272
1610.767
1620.604
1630.929
1640.434
1650.174
1660.825
1670.724
1680.304
1690.0164
170.114
180.433
190.158
20.342
200.78
210.796
220.132
230.00656
240.188
250.45
260.32
270.119
280.927
290.368
30.086
300.466
310.579
320.0331
330.453
340.473
350.46
360.192
370.0331
380.308
390.235
40.937
400.229
410.105
420.295
430.133
440.403
450.373
460.263
470.344
480.288
490.228
50.0841
500.443
510.319
520.288
530.449
540.185
550.0111
560.464
570.578
580.186
590.0317
60.745
600.0598
610.352
620.0553
630.131
640.726
650.137
660.645
670.471
680.789
690.523
70.223
700.024
710.143
720.138
730.0292
740.38
750.0984
760.865
770.0622
780.174
790.324
80.227
800.129
810.577
820.0499
830.0935
840.766
850.00805
860.266
870.391
880.939
890.0899
90.148
900.314
910.16
920.0407
930.761
940.141
950.0702
960.0638
970.784
980.32
990.447



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: CNhs11747


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
154 (mixed cell type cancer)
162 (cancer)
305 (carcinoma)
4 (disease)
4236 (carcinosarcoma)

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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