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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000025,UBERON:0000055,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000119,UBERON:0000353,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001009,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001280,UBERON:0001281,UBERON:0001434,UBERON:0001474,UBERON:0001555,UBERON:0001981,UBERON:0002049,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002193,UBERON:0002204,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003081,UBERON:0003104,UBERON:0003497,UBERON:0003513,UBERON:0003835,UBERON:0003894,UBERON:0003909,UBERON:0003914,UBERON:0004111,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004535,UBERON:0004537,UBERON:0004647,UBERON:0004765,UBERON:0004872,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0005911,UBERON:0006235,UBERON:0006925,UBERON:0006965,UBERON:0007026,UBERON:0007500,UBERON:0007798,UBERON:0008835,UBERON:0008836,UBERON:0009142
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100224
|fonse_cell_line=FF:0100224
|fonse_cell_line_closure=FF:0100224
|fonse_cell_line_closure=FF:0100224

Revision as of 16:57, 29 March 2012


Name:hepatic mesenchymal tumor cell line:LI90
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexfemale
age55
cell typeadipocyte, lipocyte of liver
cell lineLI90
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-penis0.0773
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-0.295
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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: CNhs11868

Jaspar motifP-value
MA0002.20.277
MA0003.10.976
MA0004.10.0143
MA0006.10.247
MA0007.10.917
MA0009.10.305
MA0014.10.254
MA0017.10.165
MA0018.23.75211e-4
MA0019.10.456
MA0024.12.42038e-8
MA0025.10.0211
MA0027.10.249
MA0028.12.9846e-5
MA0029.10.501
MA0030.10.129
MA0031.10.209
MA0035.20.0541
MA0038.12.69328e-4
MA0039.21.74438e-5
MA0040.10.523
MA0041.10.845
MA0042.10.797
MA0043.16.01969e-4
MA0046.10.185
MA0047.20.965
MA0048.10.057
MA0050.10.037
MA0051.10.0109
MA0052.10.211
MA0055.10.349
MA0057.10.75
MA0058.13.70481e-5
MA0059.10.0478
MA0060.13.10758e-14
MA0061.10.148
MA0062.22.43081e-14
MA0065.20.083
MA0066.10.799
MA0067.10.0252
MA0068.10.507
MA0069.10.33
MA0070.10.676
MA0071.10.967
MA0072.10.746
MA0073.10.261
MA0074.10.827
MA0076.13.20302e-7
MA0077.10.769
MA0078.10.521
MA0079.20.866
MA0080.24.11664e-8
MA0081.15.95943e-4
MA0083.13.3861e-4
MA0084.10.777
MA0087.10.822
MA0088.10.0119
MA0090.11.5875e-5
MA0091.10.0986
MA0092.10.00888
MA0093.10.00615
MA0099.20.0755
MA0100.10.123
MA0101.10.236
MA0102.20.0515
MA0103.10.0154
MA0104.21.92545e-4
MA0105.10.0605
MA0106.10.0415
MA0107.10.429
MA0108.20.358
MA0111.10.335
MA0112.20.238
MA0113.10.835
MA0114.10.142
MA0115.10.077
MA0116.10.331
MA0117.10.233
MA0119.10.0181
MA0122.10.605
MA0124.10.204
MA0125.10.213
MA0131.10.0867
MA0135.10.151
MA0136.11.75954e-11
MA0137.20.0175
MA0138.20.62
MA0139.10.249
MA0140.10.321
MA0141.10.252
MA0142.10.168
MA0143.10.653
MA0144.10.995
MA0145.10.691
MA0146.10.37
MA0147.10.0027
MA0148.10.763
MA0149.10.534
MA0150.10.327
MA0152.10.124
MA0153.10.41
MA0154.10.604
MA0155.10.311
MA0156.12.26646e-9
MA0157.10.559
MA0159.10.704
MA0160.10.154
MA0162.10.412
MA0163.10.855
MA0164.10.367
MA0258.10.274
MA0259.10.109



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: CNhs11868

Novel motifP-value
10.797
100.69
1000.499
1010.631
1020.133
1030.449
1040.564
1050.28
1060.00377
1070.00916
1080.423
1090.813
110.575
1100.468
1110.604
1120.429
1130.553
1140.214
1150.239
1160.0206
1170.261
1180.757
1190.0893
120.138
1200.402
1210.443
1220.142
1230.941
1240.655
1250.875
1260.632
1270.938
1280.0527
1290.352
130.0822
1300.508
1310.188
1320.517
1330.932
1340.637
1350.429
1360.379
1370.473
1380.736
1390.034
140.311
1400.476
1410.566
1420.712
1430.75
1440.509
1450.812
1460.269
1470.135
1480.938
1490.00502
150.692
1500.0609
1510.468
1520.0338
1530.63
1540.354
1550.0467
1560.415
1570.532
1580.13
1590.461
160.0937
1600.655
1610.978
1620.864
1630.551
1640.0466
1650.591
1660.037
1670.911
1680.482
1690.405
170.271
180.24
190.0761
20.161
200.403
210.421
220.637
230.005
240.316
250.139
260.498
270.974
280.416
290.465
30.545
300.724
310.392
322.84197e-14
330.183
340.674
350.921
360.0814
370.781
380.81
390.523
40.679
400.181
410.955
420.64
430.479
440.704
450.937
460.183
470.672
480.672
490.426
50.172
500.636
510.94
520.263
530.858
540.401
550.168
560.853
570.226
580.538
590.389
60.462
600.225
610.399
620.617
630.19
640.938
650.323
660.172
670.191
680.794
690.619
70.277
700.263
710.919
720.435
730.0756
740.0839
750.249
760.991
770.0684
780.988
790.0015
80.29
800.204
810.854
820.0927
830.592
840.789
859.40643e-4
860.916
870.832
880.608
890.352
90.778
900.452
910.538
920.0146
930.915
940.197
950.737
960.684
970.26
980.246
990.0192



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: CNhs11868


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)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000235 (macrophage)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000864 (tissue-resident macrophage)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
3118 (hepatobiliary disease)
4 (disease)
409 (liver disease)
7 (disease of anatomical entity)
77 (gastrointestinal system disease)

UBERON: Anatomy
0000015 (anatomical boundary)
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000353 (parenchyma)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001009 (circulatory system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001280 (liver parenchyma)
0001281 (hepatic sinusoid)
0001434 (skeletal system)
0001474 (bone element)
0001555 (digestive tract)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003497 (abdomen blood vessel)
0003513 (trunk blood vessel)
0003835 (abdominal segment blood vessel)
0003894 (liver primordium)
0003909 (sinusoid)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004647 (liver lobule)
0004765 (skeletal element)
0004872 (splanchnic layer of lateral plate mesoderm)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0006965 (vascular cord)
0007026 (primitive gut)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

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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