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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:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,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 16:58, 29 March 2012


Name:adenocarcinoma cell line:IM95m
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuestomach
dev stageNA
sexmale
age63
cell typeunclassifiable
cell lineIM95m
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-penis0.111
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-lymphoma0.412
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11882

Jaspar motifP-value
MA0002.20.0374
MA0003.10.915
MA0004.10.111
MA0006.10.231
MA0007.10.0908
MA0009.10.00508
MA0014.10.00901
MA0017.13.24118e-6
MA0018.20.875
MA0019.10.383
MA0024.17.29391e-4
MA0025.10.509
MA0027.10.949
MA0028.14.21083e-4
MA0029.10.0277
MA0030.10.162
MA0031.10.158
MA0035.20.00122
MA0038.13.70686e-4
MA0039.28.94006e-4
MA0040.10.428
MA0041.10.32
MA0042.10.582
MA0043.10.706
MA0046.11.00915e-52
MA0047.23.00636e-4
MA0048.10.25
MA0050.10.0645
MA0051.10.0207
MA0052.10.5
MA0055.10.00472
MA0057.10.227
MA0058.10.139
MA0059.10.0349
MA0060.13.87673e-14
MA0061.10.00114
MA0062.21.28638e-4
MA0065.21.49346e-4
MA0066.10.29
MA0067.10.834
MA0068.17.4824e-4
MA0069.10.167
MA0070.10.151
MA0071.10.447
MA0072.10.0588
MA0073.10.519
MA0074.10.774
MA0076.10.00858
MA0077.10.84
MA0078.10.145
MA0079.20.226
MA0080.20.0817
MA0081.10.075
MA0083.10.169
MA0084.10.0668
MA0087.10.717
MA0088.10.0625
MA0090.10.8
MA0091.10.0167
MA0092.10.157
MA0093.10.0766
MA0099.20.294
MA0100.10.332
MA0101.10.321
MA0102.20.313
MA0103.18.43422e-9
MA0104.20.0064
MA0105.15.71845e-6
MA0106.10.502
MA0107.10.0389
MA0108.20.627
MA0111.10.867
MA0112.20.51
MA0113.10.789
MA0114.11.10236e-12
MA0115.12.67238e-4
MA0116.10.0697
MA0117.10.88
MA0119.10.494
MA0122.10.435
MA0124.10.418
MA0125.10.0971
MA0131.10.662
MA0135.10.216
MA0136.10.755
MA0137.20.0966
MA0138.20.695
MA0139.10.194
MA0140.10.0116
MA0141.10.0503
MA0142.10.201
MA0143.10.905
MA0144.10.117
MA0145.10.291
MA0146.10.00887
MA0147.10.00976
MA0148.10.00111
MA0149.10.0497
MA0150.10.182
MA0152.10.0589
MA0153.11.4395e-22
MA0154.19.29542e-4
MA0155.10.231
MA0156.10.507
MA0157.10.539
MA0159.10.637
MA0160.10.0869
MA0162.10.745
MA0163.10.105
MA0164.10.053
MA0258.10.797
MA0259.10.191



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: CNhs11882

Novel motifP-value
10.86
100.95
1000.896
1010.376
1020.909
1030.67
1040.717
1050.279
1060.0726
1070.395
1080.505
1090.104
110.722
1100.735
1110.9
1120.467
1130.00944
1140.746
1150.624
1160.105
1170.65
1180.297
1190.55
120.877
1200.961
1210.732
1220.274
1230.0848
1240.142
1250.159
1260.126
1270.253
1280.0565
1290.505
130.0138
1300.241
1310.00541
1320.0574
1330.106
1340.0284
1350.0954
1360.00627
1370.494
1380.35
1390.313
140.888
1400.829
1410.659
1420.967
1430.0829
1440.154
1450.179
1460.539
1470.306
1480.798
1490.47
150.89
1500.678
1510.891
1520.848
1530.533
1540.79
1550.12
1560.423
1570.532
1580.934
1590.881
160.824
1600.661
1610.516
1620.351
1630.66
1640.371
1650.655
1660.564
1670.662
1680.538
1690.44
170.679
180.0672
190.303
20.823
200.553
210.68
220.673
230.0637
240.52
250.843
260.0147
270.645
280.527
290.413
30.535
300.277
310.841
320.0869
330.356
340.426
350.0198
360.436
370.346
380.264
390.836
40.792
400.164
410.115
420.988
430.497
440.505
450.852
460.456
470.981
480.993
490.257
50.547
500.705
510.851
520.485
530.273
540.837
550.552
560.77
570.448
580.511
590.286
60.279
600.92
610.135
620.866
630.841
640.653
650.528
660.00995
670.658
680.0394
690.73
70.124
700.141
710.632
720.91
730.246
740.113
750.894
760.286
770.764
780.0264
790.0124
80.57
800.369
810.181
823.79037e-5
830.719
840.199
850.202
860.873
870.0181
880.354
890.73
90.303
900.241
910.0129
920.154
930.756
940.0535
950.0336
960.343
970.805
980.467
990.659



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: CNhs11882


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)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
299 (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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