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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:small cell gastrointestinal carcinoma cell line:ECC10
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
sexunknown
ageunknown
cell typeunclassifiable
cell lineECC10
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-merkel1.019
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-penis0.449
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: CNhs11736

Jaspar motifP-value
MA0002.27.0154e-5
MA0003.10.0434
MA0004.10.834
MA0006.10.58
MA0007.10.228
MA0009.10.964
MA0014.10.29
MA0017.10.00232
MA0018.20.00459
MA0019.10.889
MA0024.14.06662e-4
MA0025.10.449
MA0027.10.458
MA0028.10.132
MA0029.10.576
MA0030.10.22
MA0031.10.418
MA0035.20.322
MA0038.10.0165
MA0039.20.621
MA0040.10.318
MA0041.10.236
MA0042.10.491
MA0043.10.0494
MA0046.10.623
MA0047.20.76
MA0048.10.721
MA0050.11.17104e-5
MA0051.19.35666e-5
MA0052.10.0819
MA0055.10.628
MA0057.10.102
MA0058.10.862
MA0059.10.608
MA0060.13.42228e-10
MA0061.10.00363
MA0062.20.386
MA0065.20.0049
MA0066.10.0431
MA0067.10.77
MA0068.10.69
MA0069.10.942
MA0070.10.199
MA0071.10.656
MA0072.10.929
MA0073.10.394
MA0074.10.366
MA0076.10.054
MA0077.10.144
MA0078.10.932
MA0079.20.454
MA0080.21.70892e-10
MA0081.10.0442
MA0083.10.0698
MA0084.10.482
MA0087.10.837
MA0088.10.964
MA0090.10.015
MA0091.10.832
MA0092.10.102
MA0093.10.942
MA0099.24.07332e-12
MA0100.10.3
MA0101.10.0177
MA0102.20.0335
MA0103.10.166
MA0104.20.834
MA0105.14.47709e-4
MA0106.10.217
MA0107.10.00349
MA0108.20.253
MA0111.10.869
MA0112.24.95063e-5
MA0113.10.0934
MA0114.10.0624
MA0115.10.648
MA0116.15.5775e-4
MA0117.10.784
MA0119.10.232
MA0122.10.357
MA0124.10.542
MA0125.10.0456
MA0131.10.209
MA0135.10.858
MA0136.14.36552e-8
MA0137.20.0451
MA0138.20.797
MA0139.10.399
MA0140.10.0494
MA0141.10.15
MA0142.10.0146
MA0143.10.285
MA0144.10.0061
MA0145.10.0592
MA0146.10.715
MA0147.10.941
MA0148.10.994
MA0149.10.202
MA0150.12.03073e-4
MA0152.10.398
MA0153.10.416
MA0154.10.00621
MA0155.10.243
MA0156.11.72582e-4
MA0157.10.877
MA0159.10.00655
MA0160.10.141
MA0162.10.171
MA0163.11.68102e-7
MA0164.10.789
MA0258.10.0144
MA0259.10.674



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: CNhs11736

Novel motifP-value
10.162
100.151
1000.85
1010.66
1020.41
1030.0374
1040.31
1050.116
1060.0058
1070.0419
1080.999
1090.221
110.133
1100.296
1110.333
1120.159
1130.157
1140.0341
1150.5
1160.263
1170.432
1180.764
1190.302
120.66
1200.556
1210.882
1220.822
1230.612
1240.255
1250.15
1260.564
1270.563
1280.0598
1290.282
130.351
1300.641
1310.518
1320.646
1330.478
1340.621
1350.00127
1360.357
1370.174
1380.793
1390.215
140.895
1400.681
1410.898
1420.996
1430.0166
1440.566
1450.303
1460.349
1470.506
1480.052
1490.121
150.0804
1500.567
1510.463
1520.0581
1530.341
1540.552
1550.624
1560.754
1570.505
1580.317
1590.0138
160.153
1600.0293
1610.527
1620.815
1630.468
1640.273
1650.183
1660.716
1670.505
1680.0601
1690.00589
170.176
180.154
190.093
20.425
200.606
210.298
220.166
230.0125
240.122
250.466
260.131
270.142
280.758
290.117
30.111
300.439
310.575
320.00612
330.256
340.255
350.305
360.56
370.126
380.477
390.171
40.735
400.65
410.141
420.253
430.0902
440.636
450.287
460.191
470.722
480.354
490.372
50.136
500.752
510.307
520.133
530.599
540.3
550.227
560.544
570.559
580.197
590.0149
60.979
600.0236
610.39
620.0417
630.235
640.301
650.172
660.284
670.803
680.421
690.432
70.371
700.11
710.112
720.0971
730.132
740.231
750.397
760.924
770.083
780.309
790.415
80.133
800.105
810.209
820.033
830.0327
840.294
850.00551
860.311
870.193
880.676
890.103
90.122
900.374
910.228
920.043
930.912
940.101
950.375
960.331
970.66
980.454
990.506



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: CNhs11736


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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