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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:0000995,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0003975,UBERON:0004120,UBERON:0004175,UBERON:0005156,UBERON:0005423,UBERON:0005795
|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:0000995,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0003100,UBERON:0003133,UBERON:0003134,UBERON:0003975,UBERON:0004120,UBERON:0004175,UBERON:0005156,UBERON:0005423,UBERON:0005795
|ancestors_in_cell_lineage_facet=CL:0000000
|ancestors_in_cell_lineage_facet=CL:0000000
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0102694
|fonse_cell_line=FF:0102694
|fonse_cell_line_closure=FF:0102694
|fonse_cell_line_closure=FF:0102694

Revision as of 16:49, 29 March 2012


Name:leiomyoma cell line:10964C
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueuterus
dev stageNA
sexfemale
ageNA
cell typesmooth muscle cell
cell lineNA
companyCoriell
collaborationNA
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-v1.4
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-penis0.0821
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-0.409
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
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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: CNhs11722

Jaspar motifP-value
MA0002.20.726
MA0003.10.199
MA0004.11
MA0006.10.133
MA0007.10.455
MA0009.10.348
MA0014.10.912
MA0017.10.653
MA0018.28.81881e-6
MA0019.10.38
MA0024.18.13293e-8
MA0025.10.00129
MA0027.10.893
MA0028.10.078
MA0029.10.956
MA0030.10.0401
MA0031.10.202
MA0035.20.691
MA0038.10.00244
MA0039.20.164
MA0040.10.566
MA0041.10.474
MA0042.10.844
MA0043.14.31992e-6
MA0046.10.421
MA0047.20.264
MA0048.10.752
MA0050.10.00112
MA0051.10.255
MA0052.10.0905
MA0055.10.317
MA0057.10.0348
MA0058.10.884
MA0059.10.569
MA0060.16.4992e-9
MA0061.10.836
MA0062.22.64567e-4
MA0065.20.108
MA0066.10.0538
MA0067.10.0153
MA0068.10.507
MA0069.10.167
MA0070.10.124
MA0071.10.21
MA0072.10.921
MA0073.10.917
MA0074.10.123
MA0076.10.0509
MA0077.10.201
MA0078.10.474
MA0079.20.72
MA0080.21.73941e-7
MA0081.10.0556
MA0083.10.0498
MA0084.10.893
MA0087.10.963
MA0088.10.897
MA0090.10.293
MA0091.10.492
MA0092.10.481
MA0093.10.964
MA0099.20.446
MA0100.10.071
MA0101.10.0107
MA0102.20.00384
MA0103.10.736
MA0104.20.326
MA0105.10.0599
MA0106.10.0717
MA0107.10.0168
MA0108.20.0386
MA0111.10.527
MA0112.20.00101
MA0113.10.818
MA0114.10.569
MA0115.10.966
MA0116.10.163
MA0117.10.669
MA0119.10.16
MA0122.10.969
MA0124.10.00908
MA0125.10.484
MA0131.10.299
MA0135.10.401
MA0136.15.53424e-10
MA0137.20.0274
MA0138.20.316
MA0139.10.205
MA0140.10.34
MA0141.10.103
MA0142.10.135
MA0143.10.151
MA0144.10.28
MA0145.10.158
MA0146.10.202
MA0147.10.561
MA0148.10.841
MA0149.10.842
MA0150.10.984
MA0152.10.796
MA0153.10.434
MA0154.10.28
MA0155.10.0852
MA0156.19.8794e-7
MA0157.10.584
MA0159.10.0614
MA0160.10.905
MA0162.10.0649
MA0163.10.00477
MA0164.10.457
MA0258.10.102
MA0259.10.69



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: CNhs11722

Novel motifP-value
10.393
100.542
1000.859
1010.794
1020.53
1030.0713
1040.615
1050.233
1060.114
1070.268
1080.213
1090.14
110.122
1100.292
1110.796
1120.0721
1130.0294
1140.0326
1150.0115
1160.062
1170.465
1180.506
1190.727
120.531
1200.107
1210.228
1220.463
1230.0173
1240.902
1250.933
1260.864
1270.744
1280.182
1290.554
130.95
1300.814
1310.412
1320.567
1330.0564
1340.351
1350.976
1360.29
1370.298
1380.934
1390.104
140.72
1400.877
1410.436
1420.947
1430.0994
1440.213
1450.546
1460.736
1470.0509
1480.108
1490.00252
150.759
1500.518
1510.417
1520.0346
1530.873
1540.654
1550.313
1560.887
1570.882
1580.0157
1590.189
160.0134
1600.208
1610.618
1620.428
1630.752
1640.125
1650.917
1660.108
1670.752
1680.639
1690.0351
170.264
180.288
190.04
20.31
200.53
210.222
220.0573
230.349
240.429
250.495
260.356
270.0888
280.275
290.109
30.272
300.41
310.315
326.09292e-6
330.832
340.816
350.206
360.0853
370.0173
380.928
390.207
40.509
400.93
410.889
420.763
430.325
440.00459
450.55
460.09
470.534
480.511
490.827
50.815
500.794
510.362
520.455
530.154
540.386
550.318
560.523
570.876
580.813
590.0301
60.951
600.419
610.913
620.736
630.318
640.686
650.211
660.601
670.567
680.381
690.192
70.285
700.00759
710.173
720.872
730.0211
740.627
750.345
760.854
770.00662
780.591
790.00727
80.03
800.214
810.236
820.0404
830.353
840.449
850.101
860.461
870.0456
880.491
890.0154
90.435
900.991
910.93
920.0536
930.404
940.805
950.257
960.934
970.947
980.616
990.0329



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: CNhs11722


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)

DOID: Disease
0060072 (benign neoplasm)
0060084 (cell type benign neoplasm)
127 (leiomyoma)
14566 (disease of cellular proliferation)
4 (disease)

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)
0000995 (uterus)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003100 (female organism)
0003133 (reproductive organ)
0003134 (female reproductive organ)
0003975 (internal female genitalia)
0004120 (mesoderm-derived structure)
0004175 (internal genitalia)
0005156 (reproductive structure)
0005423 (developing anatomical structure)
0005795 (embryonic uterus)

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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