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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,FF:0101533
|fonse_cell_line=FF:0101120,FF:0101533
|fonse_cell_line_closure=FF:0101120,FF:0101533
|fonse_cell_line_closure=FF:0101120,FF:0101533

Revision as of 16:50, 29 March 2012


Name:gastrointestinal carcinoma cell line:ECC12
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 lineECC12
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-penis0.393
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
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: CNhs11738

Jaspar motifP-value
MA0002.22.32116e-4
MA0003.10.158
MA0004.10.297
MA0006.10.328
MA0007.10.09
MA0009.10.789
MA0014.10.967
MA0017.10.392
MA0018.20.0547
MA0019.10.773
MA0024.10.00972
MA0025.10.921
MA0027.10.885
MA0028.10.124
MA0029.10.725
MA0030.10.122
MA0031.10.722
MA0035.20.784
MA0038.10.102
MA0039.20.253
MA0040.10.652
MA0041.10.396
MA0042.10.479
MA0043.10.0905
MA0046.12.162e-13
MA0047.20.0927
MA0048.10.549
MA0050.14.03136e-5
MA0051.19.9138e-4
MA0052.10.416
MA0055.10.797
MA0057.10.0536
MA0058.10.202
MA0059.10.775
MA0060.11.33967e-5
MA0061.10.00448
MA0062.20.192
MA0065.20.185
MA0066.10.198
MA0067.10.833
MA0068.10.479
MA0069.10.4
MA0070.10.0234
MA0071.10.958
MA0072.10.688
MA0073.10.282
MA0074.10.541
MA0076.10.0839
MA0077.10.285
MA0078.10.711
MA0079.20.902
MA0080.21.28481e-9
MA0081.10.0479
MA0083.10.018
MA0084.10.619
MA0087.10.211
MA0088.10.903
MA0090.13.70429e-4
MA0091.10.319
MA0092.10.101
MA0093.10.212
MA0099.22.05907e-14
MA0100.10.229
MA0101.10.0173
MA0102.20.16
MA0103.10.424
MA0104.20.277
MA0105.10.00265
MA0106.10.0677
MA0107.10.00473
MA0108.20.739
MA0111.10.906
MA0112.21.56234e-4
MA0113.10.135
MA0114.10.854
MA0115.10.0878
MA0116.10.0121
MA0117.10.756
MA0119.10.0359
MA0122.10.271
MA0124.10.431
MA0125.10.263
MA0131.10.303
MA0135.10.0563
MA0136.15.91473e-7
MA0137.20.0814
MA0138.20.97
MA0139.10.547
MA0140.10.438
MA0141.10.274
MA0142.10.325
MA0143.10.584
MA0144.10.0668
MA0145.10.0299
MA0146.10.188
MA0147.10.423
MA0148.10.335
MA0149.10.0703
MA0150.10.00508
MA0152.10.759
MA0153.14.33561e-8
MA0154.10.0147
MA0155.10.368
MA0156.10.00151
MA0157.10.791
MA0159.10.134
MA0160.10.334
MA0162.10.0651
MA0163.10.0213
MA0164.10.853
MA0258.10.0361
MA0259.10.247



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: CNhs11738

Novel motifP-value
10.183
100.328
1000.533
1010.682
1020.905
1030.0955
1040.931
1050.192
1068.59514e-4
1070.0741
1080.801
1090.144
110.0447
1100.24
1110.212
1120.338
1130.0196
1140.0783
1150.349
1160.454
1170.426
1180.99
1190.209
120.66
1200.848
1210.914
1220.673
1230.611
1240.0619
1250.454
1260.945
1270.0397
1280.0114
1290.0914
130.709
1300.0613
1310.379
1320.866
1330.631
1340.624
1350.00529
1360.499
1370.0307
1380.471
1390.27
140.632
1400.16
1410.442
1420.687
1431.76259e-4
1440.411
1450.275
1460.474
1470.978
1480.0485
1490.0612
150.167
1500.344
1510.182
1520.0424
1530.718
1540.605
1550.303
1560.863
1570.607
1580.319
1590.218
160.206
1600.0949
1610.35
1620.658
1630.76
1640.921
1650.243
1660.796
1670.743
1680.194
1690.00816
170.127
180.182
190.247
20.284
200.225
210.558
220.115
230.00853
240.18
250.756
260.292
270.109
280.883
290.459
30.132
300.214
310.732
320.0248
330.36
340.223
350.728
360.931
370.0709
380.396
390.0883
40.744
400.422
410.16
420.272
430.214
440.931
450.178
460.102
470.229
480.229
490.331
50.228
500.669
510.138
520.127
530.276
540.142
550.182
560.377
570.426
580.595
590.0938
60.53
600.0306
610.744
620.25
630.0861
640.453
650.125
660.884
670.683
680.303
690.998
70.821
700.147
710.0269
720.0988
730.123
740.257
750.479
760.765
770.107
780.361
790.433
80.202
800.236
810.209
820.119
830.0866
840.421
850.00833
860.372
870.195
880.926
890.0186
90.113
900.218
910.129
920.196
930.984
940.0444
950.41
960.117
970.816
980.429
990.673



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: CNhs11738


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
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
3119 (gastrointestinal system cancer)
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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