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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0000949,UBERON:0001062,UBERON:0001235,UBERON:0001851,UBERON:0002050,UBERON:0002100,UBERON:0002342,UBERON:0002346,UBERON:0002368,UBERON:0002369,UBERON:0002417,UBERON:0002530,UBERON:0002532,UBERON:0003075,UBERON:0004120,UBERON:0004121,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006598,UBERON:0007284
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0000949,UBERON:0001062,UBERON:0001235,UBERON:0001851,UBERON:0002050,UBERON:0002100,UBERON:0002342,UBERON:0002346,UBERON:0002368,UBERON:0002369,UBERON:0002417,UBERON:0002530,UBERON:0002532,UBERON:0003075,UBERON:0004120,UBERON:0004121,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006598,UBERON:0007284
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000077,CL:0000144,CL:0000150,CL:0000151,CL:0000163,CL:0000174,CL:0000213,CL:0000215,CL:0000220,CL:0000222,CL:0000255,CL:0000548,CL:0002078,CL:0002097,CL:0002321,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,CL:0000077,CL:0000144,CL:0000150,CL:0000151,CL:0000163,CL:0000174,CL:0000213,CL:0000215,CL:0000220,CL:0000222,CL:0000255,CL:0000548,CL:0002078,CL:0002097,CL:0002321,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120,FF:0102424
|fonse_cell_line=FF:0101120,FF:0102424
|fonse_cell_line_closure=FF:0101120,FF:0102424
|fonse_cell_line_closure=FF:0101120,FF:0102424

Revision as of 16:41, 29 March 2012


Name:mesothelioma cell line:ACC-MESO-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuemesothelium
dev stageNA
sexfemale
age61
cell typemesothelial cell
cell lineACC-MESO-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
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-penis-0.0876
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-lymphoma0.104
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs11263

Jaspar motifP-value
MA0002.20.167
MA0003.10.64
MA0004.10.483
MA0006.10.668
MA0007.10.823
MA0009.10.58
MA0014.10.0946
MA0017.10.977
MA0018.20.344
MA0019.10.429
MA0024.10.532
MA0025.10.432
MA0027.10.778
MA0028.11.57527e-4
MA0029.10.0324
MA0030.10.0735
MA0031.10.946
MA0035.20.00726
MA0038.10.0354
MA0039.21.65383e-4
MA0040.10.992
MA0041.10.701
MA0042.10.722
MA0043.10.27
MA0046.10.815
MA0047.20.313
MA0048.10.175
MA0050.15.22881e-8
MA0051.19.58328e-9
MA0052.10.616
MA0055.15.41455e-7
MA0057.10.599
MA0058.10.829
MA0059.10.374
MA0060.14.88808e-7
MA0061.10.568
MA0062.22.65946e-4
MA0065.20.811
MA0066.10.944
MA0067.10.45
MA0068.10.0341
MA0069.10.232
MA0070.10.783
MA0071.10.483
MA0072.10.602
MA0073.10.617
MA0074.10.127
MA0076.11.95397e-5
MA0077.10.281
MA0078.10.372
MA0079.20.358
MA0080.23.28273e-10
MA0081.10.022
MA0083.10.516
MA0084.10.16
MA0087.10.123
MA0088.10.438
MA0090.10.00511
MA0091.10.136
MA0092.10.0726
MA0093.10.365
MA0099.22.94515e-6
MA0100.10.493
MA0101.10.0125
MA0102.20.0301
MA0103.10.09
MA0104.20.192
MA0105.10.155
MA0106.10.718
MA0107.10.00625
MA0108.20.0296
MA0111.10.278
MA0112.20.0362
MA0113.10.905
MA0114.10.623
MA0115.10.156
MA0116.10.00977
MA0117.10.872
MA0119.10.303
MA0122.10.634
MA0124.10.844
MA0125.10.734
MA0131.10.118
MA0135.10.0277
MA0136.15.29478e-7
MA0137.20.164
MA0138.20.00317
MA0139.10.866
MA0140.10.00719
MA0141.10.638
MA0142.10.294
MA0143.10.457
MA0144.10.944
MA0145.10.327
MA0146.10.235
MA0147.10.145
MA0148.10.574
MA0149.10.0378
MA0150.10.0269
MA0152.10.746
MA0153.10.857
MA0154.10.00896
MA0155.10.516
MA0156.10.86
MA0157.10.468
MA0159.10.577
MA0160.10.225
MA0162.10.93
MA0163.10.0126
MA0164.10.345
MA0258.10.271
MA0259.10.0766



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: CNhs11263

Novel motifP-value
10.741
100.319
1000.178
1010.0558
1020.592
1030.327
1040.79
1050.886
1060.00231
1070.153
1080.269
1090.178
110.217
1100.928
1110.156
1120.00776
1130.186
1140.957
1150.561
1160.2
1170.544
1180.0562
1190.602
120.584
1200.655
1210.516
1220.177
1230.785
1240.544
1250.167
1260.545
1270.33
1280.0289
1290.94
130.212
1300.579
1310.392
1320.658
1330.0987
1340.183
1350.137
1360.0292
1370.236
1380.306
1390.458
140.239
1400.0559
1410.722
1420.078
1430.658
1440.852
1450.00483
1460.934
1470.664
1480.646
1490.16
150.227
1500.334
1510.356
1520.352
1530.463
1540.235
1550.214
1560.337
1570.589
1580.784
1590.194
160.213
1600.174
1610.967
1620.624
1630.919
1640.32
1650.517
1660.662
1670.656
1680.254
1690.888
170.461
180.727
190.177
20.307
200.0251
210.752
220.652
230.22
240.829
250.217
260.353
270.254
280.202
290.391
30.285
300.982
310.314
320.00281
330.85
340.361
350.00132
360.118
370.842
380.33
390.977
40.565
400.0562
410.149
420.0504
430.85
440.108
450.56
460.0698
470.982
480.896
490.445
50.373
500.245
510.237
520.897
530.447
540.251
550.944
560.42
570.656
580.283
590.0327
60.354
600.0839
610.00286
620.0767
630.629
640.68
650.685
664.49061e-7
670.738
680.0729
690.36
70.559
700.816
710.464
720.696
730.227
740.765
750.266
760.245
770.23
780.726
790.13
80.396
800.278
810.331
820.378
830.241
840.431
850.34
860.155
870.15
880.71
890.25
90.089
900.698
910.113
920.945
930.589
940.975
950.338
960.997
970.137
980.0908
990.6



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: CNhs11263


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)
0000076 (squamous epithelial cell)
0000077 (mesothelial cell)
0000150 (glandular epithelial cell)
0000151 (secretory cell)
0000163 (endocrine cell)
0000174 (steroid hormone secreting cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002097 (cortical cell of adrenal gland)
0002321 (embryonic cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
170 (endocrine gland cancer)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001062 (anatomical entity)
0001235 (adrenal cortex)
0001851 (cortex)
0002050 (embryonic structure)
0002100 (trunk)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002369 (adrenal gland)
0002417 (abdominal segment of trunk)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007284 (presumptive neural plate)

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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