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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0004120,UBERON:0005156,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0004120,UBERON:0005156,UBERON:0005423
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:10689-109F5
|fonse_cell_line=FF:10689-109F5
|fonse_cell_line_closure=FF:10689-109F5
|fonse_cell_line_closure=FF:10689-109F5

Revision as of 17:02, 29 March 2012


Name:mixed mullerian tumor cell line:HTMMT
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueendometrium
dev stageNA
sexfemale
age66
cell typeunclassifiable
cell lineHTMMT
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-penis0.256
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-lymphoma0.215
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: CNhs11944

Jaspar motifP-value
MA0002.20.832
MA0003.10.516
MA0004.10.34
MA0006.10.671
MA0007.10.265
MA0009.10.645
MA0014.10.726
MA0017.10.237
MA0018.20.00194
MA0019.10.313
MA0024.10.0824
MA0025.10.0187
MA0027.10.261
MA0028.10.473
MA0029.10.282
MA0030.10.00137
MA0031.10.00837
MA0035.20.0135
MA0038.10.214
MA0039.20.0155
MA0040.10.0259
MA0041.10.0584
MA0042.10.349
MA0043.18.97837e-4
MA0046.10.00285
MA0047.20.0229
MA0048.10.0124
MA0050.10.0522
MA0051.10.0434
MA0052.14.40443e-7
MA0055.10.0183
MA0057.10.764
MA0058.10.7
MA0059.10.0494
MA0060.10.835
MA0061.10.46
MA0062.20.118
MA0065.20.0741
MA0066.10.28
MA0067.10.503
MA0068.10.806
MA0069.10.415
MA0070.10.815
MA0071.10.22
MA0072.10.88
MA0073.10.841
MA0074.10.269
MA0076.10.508
MA0077.10.922
MA0078.10.551
MA0079.20.00247
MA0080.22.38249e-11
MA0081.10.0118
MA0083.10.614
MA0084.10.863
MA0087.10.113
MA0088.10.391
MA0090.10.969
MA0091.10.718
MA0092.10.703
MA0093.10.406
MA0099.21.81361e-9
MA0100.10.934
MA0101.10.119
MA0102.20.00289
MA0103.10.309
MA0104.20.386
MA0105.10.06
MA0106.10.925
MA0107.10.0316
MA0108.24.69578e-8
MA0111.10.399
MA0112.20.0196
MA0113.10.624
MA0114.10.862
MA0115.10.418
MA0116.10.112
MA0117.10.487
MA0119.10.0303
MA0122.10.391
MA0124.10.0203
MA0125.10.413
MA0131.10.91
MA0135.10.0188
MA0136.11.17171e-11
MA0137.20.0953
MA0138.20.876
MA0139.10.318
MA0140.10.0306
MA0141.10.169
MA0142.10.478
MA0143.10.987
MA0144.10.159
MA0145.10.139
MA0146.10.384
MA0147.10.186
MA0148.10.134
MA0149.10.115
MA0150.10.0469
MA0152.10.208
MA0153.10.543
MA0154.10.41
MA0155.10.85
MA0156.16.02672e-9
MA0157.10.222
MA0159.10.0487
MA0160.10.485
MA0162.10.153
MA0163.10.00161
MA0164.10.852
MA0258.10.0027
MA0259.10.165



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: CNhs11944

Novel motifP-value
10.0625
100.0277
1000.0176
1010.784
1020.75
1030.291
1040.998
1050.00869
1060.746
1070.0568
1080.2
1090.242
110.266
1100.176
1110.00854
1120.98
1130.0078
1140.0977
1150.0092
1160.146
1170.0314
1180.367
1190.327
120.201
1200.512
1210.324
1220.142
1230.141
1240.453
1250.298
1260.718
1270.929
1280.725
1290.666
130.0235
1300.0731
1310.643
1320.757
1330.0674
1340.165
1350.0225
1360.0756
1370.188
1380.939
1390.991
140.407
1400.619
1410.18
1420.705
1430.514
1440.927
1450.624
1460.742
1470.131
1480.706
1490.688
150.247
1500.0569
1510.978
1520.258
1530.38
1540.689
1550.617
1560.858
1570.419
1580.0722
1590.225
160.0792
1600.743
1610.644
1620.0711
1630.71
1640.0705
1650.712
1660.349
1670.0359
1680.121
1690.821
170.877
180.128
190.135
20.226
200.144
210.144
220.455
230.644
240.946
250.588
260.0923
270.482
280.85
290.0645
30.445
300.209
310.531
326.14773e-7
330.082
340.45
350.121
360.265
370.0514
380.953
390.728
40.755
400.199
410.242
420.942
430.401
440.0976
450.142
460.242
470.102
480.215
490.584
50.944
500.862
510.8
520.57
530.314
540.76
550.278
560.596
570.223
580.469
590.665
60.437
600.749
610.255
620.886
630.281
640.217
650.771
660.569
670.224
680.806
690.365
70.971
700.37
710.0433
720.81
730.363
740.549
750.024
760.294
770.457
780.52
790.0979
80.0874
800.00905
810.299
820.845
830.858
840.817
850.709
860.775
870.0127
880.899
890.796
90.138
900.125
910.95
920.927
930.785
940.665
950.283
960.552
970.874
980.965
990.28



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: CNhs11944


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
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
154 (mixed cell type cancer)
162 (cancer)
4 (disease)
4236 (carcinosarcoma)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000474 (female reproductive system)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000990 (reproductive system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0004120 (mesoderm-derived structure)
0005156 (reproductive structure)
0005423 (developing anatomical structure)

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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