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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:0000076,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000076,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 16:41, 29 March 2012


Name:squamous cell carcinoma cell line:EC-GI-10
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueesophagus
dev stageNA
sexmale
age65
cell typeunclassifiable
cell lineEC-GI-10
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-penis0.0539
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-lymphoma0.158
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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 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: CNhs11252

Jaspar motifP-value
MA0002.20.0021
MA0003.10.308
MA0004.10.764
MA0006.10.216
MA0007.10.85
MA0009.10.139
MA0014.10.0283
MA0017.10.704
MA0018.20.904
MA0019.10.547
MA0024.10.154
MA0025.10.334
MA0027.10.717
MA0028.10.00199
MA0029.10.884
MA0030.10.00271
MA0031.10.0759
MA0035.20.157
MA0038.10.265
MA0039.23.64803e-4
MA0040.10.429
MA0041.10.639
MA0042.10.58
MA0043.10.384
MA0046.10.9
MA0047.20.00834
MA0048.10.309
MA0050.10.0155
MA0051.10.00656
MA0052.10.034
MA0055.14.13523e-4
MA0057.10.791
MA0058.10.655
MA0059.10.791
MA0060.10.0628
MA0061.10.732
MA0062.20.0153
MA0065.20.629
MA0066.10.413
MA0067.10.945
MA0068.10.00819
MA0069.10.337
MA0070.10.91
MA0071.10.213
MA0072.10.596
MA0073.10.807
MA0074.10.785
MA0076.10.00668
MA0077.10.269
MA0078.10.73
MA0079.20.945
MA0080.22.88567e-5
MA0081.10.00327
MA0083.10.055
MA0084.10.482
MA0087.10.715
MA0088.10.148
MA0090.10.561
MA0091.10.00511
MA0092.10.235
MA0093.10.825
MA0099.20.0381
MA0100.10.556
MA0101.10.371
MA0102.20.294
MA0103.19.82341e-10
MA0104.20.885
MA0105.10.0057
MA0106.10.00258
MA0107.10.521
MA0108.20.949
MA0111.10.597
MA0112.20.956
MA0113.10.0638
MA0114.10.459
MA0115.11
MA0116.10.138
MA0117.10.454
MA0119.10.205
MA0122.10.731
MA0124.10.352
MA0125.10.138
MA0131.10.683
MA0135.10.111
MA0136.10.00184
MA0137.20.349
MA0138.20.201
MA0139.10.289
MA0140.10.322
MA0141.10.653
MA0142.10.0907
MA0143.10.925
MA0144.10.337
MA0145.10.548
MA0146.10.485
MA0147.10.659
MA0148.11.86389e-4
MA0149.10.0329
MA0150.10.162
MA0152.10.539
MA0153.10.929
MA0154.10.0383
MA0155.10.139
MA0156.10.349
MA0157.10.324
MA0159.10.0133
MA0160.10.762
MA0162.10.885
MA0163.10.0908
MA0164.10.749
MA0258.10.612
MA0259.10.85



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: CNhs11252

Novel motifP-value
10.706
100.73
1000.235
1010.425
1020.53
1030.879
1040.446
1050.214
1060.874
1070.3
1080.479
1090.0529
110.638
1100.896
1110.922
1120.826
1130.444
1140.324
1150.638
1160.313
1170.133
1180.954
1190.321
120.101
1200.933
1210.695
1220.46
1230.527
1240.15
1250.723
1260.331
1270.687
1280.416
1290.539
130.00287
1300.639
1310.177
1320.809
1330.0111
1340.0558
1350.075
1360.0552
1370.0186
1380.698
1390.2
140.748
1400.732
1410.606
1420.769
1430.0375
1440.235
1450.905
1460.849
1470.183
1480.601
1490.0976
150.946
1500.234
1510.801
1520.185
1530.716
1540.188
1550.226
1560.97
1570.86
1580.262
1590.44
160.933
1600.166
1610.501
1620.781
1630.46
1640.464
1650.739
1660.904
1670.514
1680.965
1690.523
170.317
180.544
190.111
20.644
200.0627
210.235
220.341
230.68
240.356
250.645
260.727
270.333
280.263
290.159
30.76
300.715
310.232
320.00299
330.371
340.309
350.126
360.383
370.907
380.957
390.304
40.718
400.116
410.00538
420.272
430.434
440.887
450.865
460.585
470.826
480.517
490.129
50.754
500.338
510.941
520.802
530.845
540.882
550.919
560.781
570.23
580.833
590.147
60.544
600.739
610.183
620.541
630.471
640.689
650.452
660.0247
670.629
680.0576
690.488
70.791
700.0351
710.777
720.565
730.403
740.0637
750.32
760.4
770.733
780.201
790.109
80.55
800.0385
810.233
820.0559
830.945
840.717
850.4
860.505
870.0458
880.483
890.537
90.144
900.79
910.11
920.155
930.493
940.245
950.326
960.371
970.984
980.0787
990.692



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: CNhs11252


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)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
1749 (squamous cell carcinoma)
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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