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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000344,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000479,UBERON:0000480,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:0004923,UBERON:0005156,UBERON:0005423,UBERON:0005564,UBERON:0009117,UBERON:0009196
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000344,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000479,UBERON:0000480,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:0004923,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: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: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 16:58, 29 March 2012


Name:mucinous cystadenocarcinoma cell line:MCAS
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
ageunknown
cell typeunclassifiable
cell lineMCAS
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-penis0.02
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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: CNhs11873

Jaspar motifP-value
MA0002.20.558
MA0003.10.978
MA0004.10.0619
MA0006.10.22
MA0007.10.94
MA0009.10.219
MA0014.10.156
MA0017.10.435
MA0018.20.337
MA0019.10.349
MA0024.10.001
MA0025.10.0218
MA0027.10.898
MA0028.10.0115
MA0029.10.105
MA0030.10.0322
MA0031.10.187
MA0035.27.0002e-5
MA0038.10.831
MA0039.20.0195
MA0040.10.756
MA0041.10.304
MA0042.10.934
MA0043.10.798
MA0046.10.133
MA0047.20.0288
MA0048.10.622
MA0050.10.0253
MA0051.10.61
MA0052.10.466
MA0055.10.00326
MA0057.10.22
MA0058.10.0439
MA0059.10.2
MA0060.10.522
MA0061.10.428
MA0062.20.00809
MA0065.20.319
MA0066.10.656
MA0067.10.656
MA0068.10.41
MA0069.10.661
MA0070.10.812
MA0071.10.524
MA0072.10.799
MA0073.10.728
MA0074.10.391
MA0076.10.0789
MA0077.10.916
MA0078.10.533
MA0079.20.706
MA0080.20.185
MA0081.10.472
MA0083.10.238
MA0084.10.297
MA0087.10.379
MA0088.10.313
MA0090.16.307e-4
MA0091.10.0283
MA0092.10.123
MA0093.10.0696
MA0099.21.6142e-17
MA0100.10.851
MA0101.10.87
MA0102.20.979
MA0103.11.33447e-12
MA0104.20.285
MA0105.10.0122
MA0106.10.898
MA0107.10.992
MA0108.20.921
MA0111.10.842
MA0112.20.901
MA0113.10.707
MA0114.10.0854
MA0115.10.202
MA0116.10.0303
MA0117.10.611
MA0119.10.618
MA0122.10.565
MA0124.10.881
MA0125.10.187
MA0131.10.891
MA0135.10.284
MA0136.10.942
MA0137.20.11
MA0138.20.0137
MA0139.10.883
MA0140.10.0464
MA0141.10.912
MA0142.10.342
MA0143.10.625
MA0144.10.488
MA0145.10.27
MA0146.10.168
MA0147.10.187
MA0148.10.00461
MA0149.10.144
MA0150.10.0366
MA0152.10.228
MA0153.10.0544
MA0154.10.043
MA0155.10.178
MA0156.10.384
MA0157.10.695
MA0159.10.241
MA0160.10.106
MA0162.10.836
MA0163.10.011
MA0164.10.685
MA0258.10.79
MA0259.10.737



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: CNhs11873

Novel motifP-value
10.581
100.956
1000.885
1010.0491
1020.403
1030.391
1040.524
1050.063
1060.0745
1070.104
1080.388
1090.00427
110.62
1100.756
1110.465
1120.385
1130.0373
1140.65
1150.813
1160.25
1170.621
1180.568
1190.582
120.673
1200.602
1210.947
1220.015
1230.62
1240.0892
1250.949
1260.385
1270.278
1280.918
1290.592
130.0757
1300.415
1310.512
1320.857
1330.12
1340.0987
1350.0274
1360.112
1370.332
1380.789
1390.665
140.967
1400.794
1410.246
1420.671
1430.22
1440.0383
1450.73
1460.492
1470.0562
1480.138
1490.207
150.179
1500.256
1510.816
1520.0254
1530.628
1540.96
1550.773
1560.225
1570.685
1580.672
1590.767
160.101
1600.949
1610.798
1620.99
1630.159
1640.439
1650.585
1660.122
1670.847
1680.478
1690.177
170.231
180.625
190.261
20.691
200.13
210.503
220.912
230.842
240.681
250.856
260.148
270.723
280.35
290.992
30.538
300.492
310.472
320.00728
330.0924
340.644
350.105
360.591
370.821
380.311
390.617
40.285
400.498
410.129
420.816
430.787
440.412
450.479
460.87
470.829
480.829
490.664
50.668
500.14
510.885
520.541
530.386
540.846
550.536
560.937
570.365
580.829
590.708
60.0255
600.19
610.189
620.649
630.117
640.973
650.562
660.0479
670.569
680.03
690.047
70.552
700.862
710.287
720.0556
730.0108
740.367
750.412
760.685
770.389
780.08
790.00327
80.958
800.556
810.0252
820.00638
830.253
840.465
850.361
860.549
870.0254
880.413
890.773
90.62
900.978
910.108
920.804
930.392
940.46
950.236
960.227
970.964
980.341
990.397



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: CNhs11873


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)
14566 (disease of cellular proliferation)
162 (cancer)
299 (adenocarcinoma)
305 (carcinoma)
3111 (cystadenocarcinoma)
3603 (mucinous cystadenocarcinoma)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000344 (mucosa)
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)
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)
0004923 (organ component layer)
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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