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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:0000034,CL:0000048,CL:0000063,CL:0000066,CL:0000144,CL:0000150,CL:0000151,CL:0000163,CL:0000164,CL:0000167,CL:0000172,CL:0000173,CL:0000255,CL:0000502,CL:0000548,CL:0000723,CL:0002351,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000066,CL:0000144,CL:0000150,CL:0000151,CL:0000163,CL:0000164,CL:0000167,CL:0000172,CL:0000173,CL:0000255,CL:0000502,CL:0000548,CL:0000723,CL:0002351,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:10781-110G7
|fonse_cell_line=FF:10781-110G7
|fonse_cell_line_closure=FF:10781-110G7
|fonse_cell_line_closure=FF:10781-110G7

Revision as of 16:58, 29 March 2012


Name:somatostatinoma cell line:QGP-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepancreas
dev stageNA
sexfemale
ageunknown
cell typepancreatic delta cell
cell lineQGP-1
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
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-lymphoma-0.145
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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-teratocarcinoma0.0919
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: CNhs11869

Jaspar motifP-value
MA0002.22.49381e-5
MA0003.10.268
MA0004.10.135
MA0006.10.579
MA0007.10.497
MA0009.10.842
MA0014.10.774
MA0017.10.0597
MA0018.22.2367e-6
MA0019.10.599
MA0024.10.69
MA0025.10.0336
MA0027.10.581
MA0028.10.016
MA0029.10.406
MA0030.12.47942e-4
MA0031.10.0111
MA0035.20.726
MA0038.10.0313
MA0039.20.534
MA0040.10.525
MA0041.10.0228
MA0042.10.216
MA0043.10.00409
MA0046.10.253
MA0047.28.79593e-4
MA0048.10.225
MA0050.13.91529e-9
MA0051.11.89812e-5
MA0052.10.369
MA0055.10.276
MA0057.10.274
MA0058.10.15
MA0059.10.904
MA0060.15.88962e-5
MA0061.10.00278
MA0062.28.26194e-4
MA0065.20.017
MA0066.10.0497
MA0067.10.869
MA0068.10.399
MA0069.10.301
MA0070.10.0626
MA0071.10.834
MA0072.10.553
MA0073.10.728
MA0074.10.201
MA0076.17.2779e-4
MA0077.10.144
MA0078.10.426
MA0079.20.28
MA0080.24.60793e-5
MA0081.10.0236
MA0083.10.388
MA0084.10.644
MA0087.10.517
MA0088.10.493
MA0090.10.00171
MA0091.10.242
MA0092.10.0356
MA0093.10.0935
MA0099.21.0969e-4
MA0100.10.775
MA0101.10.0119
MA0102.20.707
MA0103.19.91231e-6
MA0104.20.558
MA0105.16.31993e-5
MA0106.10.656
MA0107.10.00476
MA0108.20.0305
MA0111.10.662
MA0112.27.84307e-4
MA0113.10.0696
MA0114.10.154
MA0115.10.335
MA0116.10.00137
MA0117.10.58
MA0119.10.0498
MA0122.10.387
MA0124.10.699
MA0125.10.0152
MA0131.10.313
MA0135.10.844
MA0136.10.1
MA0137.20.0756
MA0138.20.825
MA0139.10.655
MA0140.10.243
MA0141.10.218
MA0142.10.167
MA0143.10.668
MA0144.10.197
MA0145.10.579
MA0146.10.302
MA0147.10.838
MA0148.10.00401
MA0149.10.193
MA0150.10.508
MA0152.10.356
MA0153.10.743
MA0154.10.00119
MA0155.10.184
MA0156.10.793
MA0157.10.249
MA0159.10.115
MA0160.10.822
MA0162.10.066
MA0163.11.35779e-6
MA0164.10.0635
MA0258.10.00825
MA0259.10.413



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: CNhs11869

Novel motifP-value
10.244
100.121
1000.442
1010.604
1020.159
1030.00841
1040.467
1050.948
1060.131
1070.271
1080.408
1090.0439
110.109
1100.12
1110.5
1120.169
1130.575
1140.0544
1150.825
1160.436
1170.0854
1180.129
1190.0957
120.585
1200.551
1210.0618
1220.309
1230.617
1240.943
1250.315
1260.285
1270.476
1280.394
1290.569
130.0732
1300.553
1310.586
1320.757
1330.99
1340.801
1350.0249
1360.9
1370.0161
1380.866
1390.923
140.568
1400.896
1410.381
1420.337
1430.0332
1440.147
1450.0446
1460.506
1470.492
1480.0744
1490.123
150.369
1500.344
1510.336
1520.38
1530.294
1540.868
1550.741
1560.715
1570.439
1580.411
1590.7
160.209
1600.00483
1610.0462
1620.891
1630.878
1640.0777
1650.219
1660.0158
1670.367
1680.0187
1690.0531
170.248
180.715
190.0742
20.699
200.915
210.0476
220.134
230.159
240.0646
250.493
260.271
270.396
280.608
290.14
30.0412
300.777
310.799
320.00576
330.15
340.135
350.196
360.099
370.0902
380.37
390.0409
40.849
400.0727
410.199
420.247
430.0728
440.494
450.69
460.32
470.283
480.232
490.149
50.324
500.401
510.4
520.588
530.433
540.782
550.752
560.87
570.524
580.365
590.0147
60.648
600.232
610.407
620.1
630.11
640.785
650.233
660.481
670.709
680.872
690.577
70.615
700.0255
710.0561
720.195
730.248
740.182
750.226
760.807
770.0536
780.432
790.0255
80.081
800.0349
810.127
820.0264
830.165
840.406
850.211
860.542
870.75
880.409
890.126
90.143
900.541
910.176
920.52
930.782
940.387
950.136
960.127
970.808
980.714
990.586



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: CNhs11869


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)
0000066 (epithelial cell)
0000150 (glandular epithelial cell)
0000151 (secretory cell)
0000163 (endocrine cell)
0000164 (enteroendocrine cell)
0000167 (peptide hormone secreting cell)
0000172 (somatostatin secreting cell)
0000173 (pancreatic D cell)
0000255 (eukaryotic cell)
0000502 (type D enteroendocrine cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002351 (progenitor cell of endocrine pancreas)
0002371 (somatic cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
169 (neuroendocrine tumor)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)
4430 (somatostatinoma)

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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