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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100400,FF:0100453,FF:0101533
|fonse_cell_line=FF:0100400,FF:0100453,FF:0101533
|fonse_cell_line_closure=FF:0100400,FF:0100453,FF:0101533
|fonse_cell_line_closure=FF:0100400,FF:0100453,FF:0101533

Revision as of 16:55, 29 March 2012


Name:carcinoid cell line:NCI-H1770
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexmale
age57
cell typeneuroendocrine cell
cell lineNCI-H1770
companyATCC
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-penis0.152
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-lymphoma0.572
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
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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: CNhs11834

Jaspar motifP-value
MA0002.21.93616e-6
MA0003.10.236
MA0004.10.473
MA0006.10.0879
MA0007.10.35
MA0009.10.627
MA0014.10.277
MA0017.10.00558
MA0018.20.0134
MA0019.10.0714
MA0024.13.65904e-8
MA0025.10.3
MA0027.10.783
MA0028.10.18
MA0029.10.905
MA0030.10.229
MA0031.10.019
MA0035.20.73
MA0038.10.00445
MA0039.20.156
MA0040.10.232
MA0041.10.346
MA0042.10.439
MA0043.10.306
MA0046.10.0215
MA0047.20.0172
MA0048.10.598
MA0050.11.67041e-8
MA0051.11.94884e-5
MA0052.10.204
MA0055.10.0596
MA0057.10.307
MA0058.10.444
MA0059.10.233
MA0060.12.05055e-16
MA0061.10.00419
MA0062.20.584
MA0065.20.0726
MA0066.10.478
MA0067.10.624
MA0068.10.57
MA0069.10.93
MA0070.10.484
MA0071.10.686
MA0072.10.664
MA0073.10.0542
MA0074.10.306
MA0076.10.0682
MA0077.10.129
MA0078.10.704
MA0079.20.232
MA0080.21.42507e-10
MA0081.10.00849
MA0083.14.26304e-5
MA0084.10.386
MA0087.10.409
MA0088.10.0951
MA0090.10.00689
MA0091.10.576
MA0092.10.184
MA0093.10.437
MA0099.26.47075e-16
MA0100.10.133
MA0101.10.00266
MA0102.20.00489
MA0103.10.0315
MA0104.20.0176
MA0105.10.0141
MA0106.10.497
MA0107.12.57504e-4
MA0108.20.0752
MA0111.10.749
MA0112.20.00413
MA0113.10.0832
MA0114.10.142
MA0115.10.29
MA0116.10.0614
MA0117.10.645
MA0119.10.706
MA0122.10.309
MA0124.10.372
MA0125.10.45
MA0131.10.341
MA0135.10.463
MA0136.13.04869e-9
MA0137.20.00521
MA0138.20.238
MA0139.10.411
MA0140.10.571
MA0141.10.188
MA0142.10.643
MA0143.10.186
MA0144.11.67769e-4
MA0145.10.0581
MA0146.10.218
MA0147.10.0329
MA0148.10.0942
MA0149.10.766
MA0150.10.00132
MA0152.10.718
MA0153.10.012
MA0154.10.117
MA0155.10.165
MA0156.11.36352e-6
MA0157.10.0363
MA0159.10.105
MA0160.10.126
MA0162.10.299
MA0163.10.00741
MA0164.10.864
MA0258.10.274
MA0259.10.0335



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: CNhs11834

Novel motifP-value
10.902
100.29
1000.196
1010.823
1020.531
1030.0445
1040.507
1050.781
1061.97329e-4
1070.0166
1080.799
1090.399
110.657
1100.772
1110.911
1120.106
1130.672
1140.227
1150.98
1160.892
1170.543
1180.845
1190.425
120.62
1200.135
1210.465
1220.783
1232.41649e-4
1240.477
1250.883
1260.194
1270.252
1280.0378
1290.607
130.726
1300.529
1310.623
1320.805
1330.0994
1340.907
1350.257
1360.796
1370.167
1380.53
1390.905
140.478
1400.272
1410.438
1420.933
1430.108
1440.573
1450.776
1460.721
1470.996
1480.0702
1490.163
150.438
1500.181
1510.386
1520.00901
1530.552
1540.503
1550.591
1560.694
1570.306
1580.868
1590.46
160.135
1600.372
1610.911
1620.434
1630.126
1640.263
1650.402
1660.996
1670.693
1680.032
1690.0654
170.191
180.22
190.134
20.163
200.385
210.527
220.0567
230.0101
240.155
250.859
260.518
270.078
280.765
290.486
30.349
300.155
310.289
320.00366
330.44
340.276
350.606
360.249
370.0693
380.77
390.314
40.306
400.143
410.0885
420.805
430.146
440.415
450.246
460.432
470.685
480.898
490.859
50.301
500.46
510.284
520.103
530.434
540.208
550.0753
560.662
570.356
580.194
590.0649
60.643
600.0111
610.485
620.0407
630.686
640.537
650.3
660.0735
670.588
680.905
690.889
70.536
700.154
710.167
720.0914
730.0141
740.455
750.236
760.963
770.2
780.572
790.15
80.436
800.0602
810.516
820.528
830.239
840.481
850.00843
860.0945
870.292
880.765
890.0249
90.0279
900.981
910.354
920.145
930.396
940.358
950.35
960.829
970.851
980.713
990.864



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: CNhs11834


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
3119 (gastrointestinal system cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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