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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000119,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000991,UBERON:0000992,UBERON:0001048,UBERON:0001062,UBERON:0002050,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0004120,UBERON:0004176,UBERON:0004458,UBERON:0004909,UBERON:0004911,UBERON:0005156,UBERON:0005423,UBERON:0005564,UBERON:0009117,UBERON:0009196
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000119,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000991,UBERON:0000992,UBERON:0001048,UBERON:0001062,UBERON:0002050,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0004120,UBERON:0004176,UBERON:0004458,UBERON:0004909,UBERON:0004911,UBERON:0005156,UBERON:0005423,UBERON:0005564,UBERON:0009117,UBERON:0009196
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000151,CL:0000159,CL:0000255,CL:0000313,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000151,CL:0000159,CL:0000255,CL:0000313,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100977,FF:0101120
|fonse_cell_line=FF:0100977,FF:0101120
|fonse_cell_line_closure=FF:0100977,FF:0101120
|fonse_cell_line_closure=FF:0100977,FF:0101120

Revision as of 16:55, 29 March 2012


Name:serous cystadenocarcinoma cell line:HTOA
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueovary
dev stageNA
sexfemale
age50
cell typeunclassifiable
cell lineHTOA
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
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-penis0.264
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-0.0436
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: CNhs11827

Jaspar motifP-value
MA0002.20.0022
MA0003.10.51
MA0004.10.158
MA0006.10.125
MA0007.10.828
MA0009.10.706
MA0014.10.0401
MA0017.10.284
MA0018.20.18
MA0019.10.046
MA0024.10.322
MA0025.10.65
MA0027.10.525
MA0028.10.268
MA0029.10.402
MA0030.10.00616
MA0031.10.0806
MA0035.20.507
MA0038.10.872
MA0039.20.0043
MA0040.10.218
MA0041.10.248
MA0042.10.219
MA0043.10.0483
MA0046.11.34523e-32
MA0047.20.973
MA0048.10.571
MA0050.10.0575
MA0051.10.355
MA0052.10.0621
MA0055.10.31
MA0057.10.697
MA0058.10.107
MA0059.10.52
MA0060.10.268
MA0061.11.07114e-5
MA0062.20.627
MA0065.20.0335
MA0066.10.745
MA0067.10.347
MA0068.10.0944
MA0069.10.323
MA0070.10.486
MA0071.10.596
MA0072.10.771
MA0073.10.806
MA0074.10.864
MA0076.10.322
MA0077.10.0043
MA0078.10.95
MA0079.20.607
MA0080.24.92023e-10
MA0081.10.0174
MA0083.10.159
MA0084.10.946
MA0087.10.505
MA0088.10.503
MA0090.10.108
MA0091.10.177
MA0092.10.678
MA0093.10.145
MA0099.20.0551
MA0100.10.858
MA0101.15.22814e-4
MA0102.20.0968
MA0103.11.79386e-9
MA0104.20.919
MA0105.13.30511e-6
MA0106.10.17
MA0107.11.67936e-4
MA0108.20.4
MA0111.10.9
MA0112.20.361
MA0113.10.143
MA0114.10.0189
MA0115.10.117
MA0116.10.105
MA0117.10.626
MA0119.10.77
MA0122.10.831
MA0124.10.799
MA0125.10.978
MA0131.10.626
MA0135.10.0351
MA0136.15.0333e-8
MA0137.20.0577
MA0138.20.365
MA0139.10.319
MA0140.10.225
MA0141.10.254
MA0142.10.205
MA0143.10.332
MA0144.10.094
MA0145.10.648
MA0146.10.017
MA0147.10.749
MA0148.10.279
MA0149.10.133
MA0150.10.403
MA0152.10.685
MA0153.15.23305e-25
MA0154.10.0345
MA0155.10.778
MA0156.12.24436e-5
MA0157.10.426
MA0159.10.039
MA0160.10.0697
MA0162.10.719
MA0163.10.0175
MA0164.10.379
MA0258.10.375
MA0259.10.748



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: CNhs11827

Novel motifP-value
10.194
100.859
1000.00791
1010.95
1020.393
1030.418
1040.753
1050.691
1060.522
1070.396
1080.643
1090.339
110.948
1100.954
1110.785
1120.588
1130.51
1140.708
1150.192
1160.892
1170.95
1180.0479
1190.31
120.409
1200.954
1210.223
1220.894
1230.0454
1240.729
1250.719
1260.772
1270.418
1280.0815
1290.157
138.2981e-4
1300.685
1310.0212
1320.783
1330.00328
1340.235
1350.00352
1360.00447
1370.116
1380.799
1390.254
140.737
1400.242
1410.755
1420.56
1430.00266
1440.908
1450.606
1460.55
1470.282
1480.137
1490.731
150.912
1500.488
1510.523
1520.604
1530.646
1540.897
1550.543
1560.889
1570.472
1580.886
1590.3
160.861
1600.928
1610.233
1620.772
1630.563
1640.617
1650.113
1660.527
1670.167
1680.0241
1690.105
170.328
180.178
190.807
20.253
200.339
210.413
220.768
230.394
240.996
250.748
260.141
270.596
280.731
290.677
30.588
300.964
310.517
320.107
330.744
340.183
350.163
360.765
370.529
380.769
390.663
40.697
400.0109
410.0205
420.509
430.941
440.474
450.766
460.832
470.711
480.776
490.803
50.224
500.852
510.677
520.679
530.806
540.651
550.443
560.717
570.222
580.754
590.273
60.962
600.487
610.539
620.6
630.708
640.893
650.376
660.516
670.958
680.345
690.231
70.05
700.887
710.878
720.838
730.37
740.145
750.974
760.169
770.233
780.681
790.358
80.558
806.77558e-4
810.314
820.505
830.0458
840.36
850.346
860.696
870.137
880.981
890.35
90.1
900.931
910.031
920.43
930.258
940.168
950.392
960.34
970.946
980.957
990.705



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: CNhs11827


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)
0000151 (secretory cell)
0000159 (seromucus secreting cell)
0000255 (eukaryotic cell)
0000313 (serous secreting cell)
0000548 (animal cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
120 (female reproductive organ cancer)
14566 (disease of cellular proliferation)
162 (cancer)
193 (reproductive organ cancer)
2152 (ovary epithelial cancer)
2394 (ovarian cancer)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0000991 (gonad)
0000992 (female gonad)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0004120 (mesoderm-derived structure)
0004176 (external genitalia)
0004458 (body cavity or lining)
0004909 (epithelium of gonad)
0004911 (epithelium of female gonad)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005564 (gonad primordium)
0009117 (indifferent gonad)
0009196 (indifferent external genitalia)

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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