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Revision as of 18:05, 27 November 2014


Name:liposarcoma cell line:KMLS-1
Species:Human (Homo sapiens)
Library ID:CNhs11870
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueretroperitoneum
dev stageNA
sexfemale
ageunknown
cell typeadipocyte
cell lineKMLS-1
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005621
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11870 CAGE DRX007920 DRR008792
Accession ID Hg19

Library idBAMCTSS
CNhs11870 DRZ000217 DRZ001602
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
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C82-Basophils-CD14-Eosinophils-Natural-Peripheral-immature-CD340
C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
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



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: CNhs11870

Jaspar motifP-value
MA0002.20.115
MA0003.10.319
MA0004.10.884
MA0006.10.562
MA0007.10.673
MA0009.10.0129
MA0014.10.375
MA0017.10.126
MA0018.20.0547
MA0019.10.397
MA0024.10.0701
MA0025.10.00366
MA0027.10.574
MA0028.10.163
MA0029.10.0684
MA0030.10.00606
MA0031.10.00566
MA0035.20.0176
MA0038.10.412
MA0039.20.00182
MA0040.10.341
MA0041.10.357
MA0042.10.888
MA0043.10.00217
MA0046.10.0431
MA0047.20.0465
MA0048.10.107
MA0050.10.0393
MA0051.10.268
MA0052.17.20182e-5
MA0055.10.792
MA0057.10.876
MA0058.10.914
MA0059.10.866
MA0060.10.0161
MA0061.18.31631e-4
MA0062.20.605
MA0065.20.00725
MA0066.10.292
MA0067.10.135
MA0068.10.0407
MA0069.10.0234
MA0070.10.135
MA0071.10.594
MA0072.10.424
MA0073.10.774
MA0074.10.689
MA0076.10.0787
MA0077.10.376
MA0078.10.239
MA0079.20.717
MA0080.21.7529e-10
MA0081.10.0976
MA0083.10.193
MA0084.10.53
MA0087.10.387
MA0088.10.7
MA0090.10.00284
MA0091.10.712
MA0092.10.997
MA0093.10.953
MA0099.27.63838e-4
MA0100.10.27
MA0101.17.16227e-4
MA0102.27.48404e-4
MA0103.16.9491e-7
MA0104.20.11
MA0105.10.00549
MA0106.10.111
MA0107.19.88759e-4
MA0108.23.3005e-5
MA0111.10.808
MA0112.20.0931
MA0113.10.794
MA0114.10.0673
MA0115.10.206
MA0116.10.0339
MA0117.10.982
MA0119.10.632
MA0122.10.389
MA0124.10.0487
MA0125.10.064
MA0131.10.549
MA0135.10.306
MA0136.11.33944e-10
MA0137.20.783
MA0138.20.911
MA0139.10.728
MA0140.10.216
MA0141.10.114
MA0142.10.106
MA0143.10.207
MA0144.10.487
MA0145.10.361
MA0146.10.441
MA0147.10.125
MA0148.10.0331
MA0149.10.635
MA0150.10.311
MA0152.10.426
MA0153.10.145
MA0154.10.00284
MA0155.10.536
MA0156.16.16546e-5
MA0157.10.043
MA0159.10.097
MA0160.10.0393
MA0162.10.938
MA0163.10.834
MA0164.10.218
MA0258.10.135
MA0259.10.821



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: CNhs11870

Novel motifP-value
10.602
100.641
1000.454
1010.786
1020.695
1030.895
1040.442
1050.29
1060.0809
1070.282
1080.115
1090.295
110.36
1100.361
1110.781
1120.836
1130.026
1140.448
1150.852
1160.279
1170.541
1180.629
1190.897
120.519
1200.968
1210.992
1220.0269
1230.881
1240.903
1250.767
1260.0452
1270.745
1280.239
1290.467
130.15
1300.541
1310.501
1320.327
1330.62
1340.863
1350.241
1360.742
1370.636
1380.906
1390.969
140.244
1400.78
1410.103
1420.951
1430.528
1440.265
1450.431
1460.0866
1470.229
1480.793
1490.922
150.0884
1500.182
1510.2
1520.897
1530.792
1540.261
1550.172
1560.54
1570.774
1580.0152
1590.158
160.369
1600.103
1610.013
1620.269
1630.297
1640.645
1650.619
1660.147
1670.488
1680.157
1690.319
170.893
180.444
190.527
20.871
200.756
210.256
220.701
230.119
240.58
250.0806
260.91
270.467
280.469
290.473
30.569
300.494
310.743
327.64878e-6
330.475
340.356
350.781
360.102
370.864
380.194
390.553
40.948
400.00726
410.209
420.445
430.455
440.807
450.21
460.861
470.583
480.582
490.252
50.608
500.824
510.529
520.202
530.729
540.559
550.0335
560.888
570.783
580.259
590.221
60.668
600.0608
610.699
620.295
630.413
640.354
650.248
660.51
670.914
680.629
690.711
70.0229
700.158
710.818
720.281
730.889
740.323
750.762
760.95
770.914
780.551
790.261
80.913
800.25
810.947
820.601
830.513
840.784
850.373
860.666
870.636
880.649
890.616
90.33
900.273
910.169
920.999
930.776
940.813
950.88
960.749
970.605
980.00588
990.312



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: CNhs11870


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

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
1115 (sarcoma)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100400 (sarcoma cell line sample)
0103744 (liposarcoma cell line sample)

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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