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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000151,CL:0000159,CL:0000255,CL:0000319,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000151,CL:0000159,CL:0000255,CL:0000319,CL:0000548
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120

Revision as of 16:51, 29 March 2012


Name:mucinous adenocarcinoma cell line:JHOM-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueovary
dev stageNA
sexfemale
age88
cell typeunclassifiable
cell lineJHOM-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-penis0.154
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-lymphoma0.369
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
C113-thyroid-throat-lung-lymph-small-colon-trachea0
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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: CNhs11752

Jaspar motifP-value
MA0002.20.392
MA0003.10.00989
MA0004.10.616
MA0006.10.322
MA0007.10.805
MA0009.10.545
MA0014.10.0181
MA0017.10.719
MA0018.20.289
MA0019.10.127
MA0024.10.0213
MA0025.10.958
MA0027.10.313
MA0028.10.23
MA0029.10.162
MA0030.10.00683
MA0031.10.0712
MA0035.20.298
MA0038.10.507
MA0039.20.918
MA0040.10.307
MA0041.10.877
MA0042.10.554
MA0043.10.888
MA0046.10.144
MA0047.20.153
MA0048.10.00965
MA0050.10.299
MA0051.10.0989
MA0052.10.032
MA0055.10.0349
MA0057.10.999
MA0058.10.343
MA0059.10.123
MA0060.10.0105
MA0061.10.938
MA0062.20.112
MA0065.20.00275
MA0066.10.904
MA0067.10.526
MA0068.10.113
MA0069.10.217
MA0070.10.248
MA0071.10.614
MA0072.10.847
MA0073.10.0739
MA0074.10.541
MA0076.10.605
MA0077.10.869
MA0078.10.633
MA0079.20.0191
MA0080.21.37493e-12
MA0081.10.0159
MA0083.10.531
MA0084.10.672
MA0087.10.514
MA0088.10.336
MA0090.10.121
MA0091.10.133
MA0092.10.609
MA0093.10.627
MA0099.25.43528e-16
MA0100.10.855
MA0101.10.864
MA0102.20.737
MA0103.10.269
MA0104.20.661
MA0105.10.102
MA0106.10.454
MA0107.10.749
MA0108.20.546
MA0111.10.4
MA0112.20.0235
MA0113.10.048
MA0114.10.0407
MA0115.10.278
MA0116.10.256
MA0117.10.992
MA0119.18.64234e-5
MA0122.10.821
MA0124.10.0704
MA0125.10.784
MA0131.10.73
MA0135.10.0164
MA0136.15.45461e-11
MA0137.20.0659
MA0138.20.0614
MA0139.10.00862
MA0140.10.83
MA0141.10.289
MA0142.10.822
MA0143.10.327
MA0144.10.595
MA0145.10.644
MA0146.10.279
MA0147.10.693
MA0148.10.537
MA0149.10.0354
MA0150.11.87882e-22
MA0152.10.717
MA0153.10.358
MA0154.10.659
MA0155.10.745
MA0156.13.58663e-5
MA0157.10.734
MA0159.10.099
MA0160.10.755
MA0162.10.038
MA0163.10.0408
MA0164.10.63
MA0258.10.272
MA0259.10.0907



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: CNhs11752

Novel motifP-value
10.0261
100.0374
1000.00685
1010.921
1020.207
1030.683
1040.836
1050.733
1060.541
1070.189
1080.987
1090.501
110.229
1100.0808
1110.465
1120.185
1130.29
1140.15
1150.453
1160.761
1170.447
1180.255
1190.292
120.497
1200.666
1210.739
1220.0445
1230.0261
1240.724
1250.191
1260.442
1270.123
1280.996
1290.723
130.0246
1300.576
1310.559
1320.523
1330.878
1340.211
1350.284
1360.00204
1370.478
1380.571
1391
140.656
1400.384
1410.242
1420.125
1430.48
1440.988
1450.988
1460.868
1470.285
1480.175
1490.251
150.0233
1500.515
1510.754
1520.809
1530.85
1540.539
1550.188
1560.749
1570.672
1580.0375
1590.0223
160.695
1600.823
1610.443
1620.343
1630.244
1640.32
1650.314
1660.585
1670.192
1680.35
1690.358
170.764
180.554
190.234
20.101
200.0277
210.119
220.388
230.438
240.903
250.904
260.183
270.0594
280.364
290.431
30.249
300.275
310.961
320.544
330.221
340.0783
350.678
360.241
370.127
380.949
390.383
40.925
400.0131
410.181
420.316
430.912
440.108
450.407
460.568
470.489
480.528
490.736
50.964
500.887
510.541
520.796
530.386
540.779
550.812
560.718
570.617
580.628
590.712
60.198
600.805
610.701
620.677
630.428
640.5
650.834
660.0533
670.725
680.289
690.286
70.472
700.383
710.0997
720.427
730.705
740.977
750.0758
760.231
770.45
780.0426
790.438
80.0562
800.00418
810.359
820.91
830.453
840.57
850.437
860.603
870.0413
880.633
890.78
90.172
900.223
910.107
920.853
930.596
940.253
950.916
960.885
970.738
980.868
990.446



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: CNhs11752


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)
0000151 (secretory cell)
0000159 (seromucus secreting cell)
0000255 (eukaryotic cell)
0000319 (mucus secreting cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
299 (adenocarcinoma)
3030 (mucinous adenocarcinoma)
305 (carcinoma)
4 (disease)

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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