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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:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000826,CL:0000837,CL:0000838,CL:0000945,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101522
|fonse_cell_line=FF:0101522
|fonse_cell_line_closure=FF:0101522
|fonse_cell_line_closure=FF:0101522

Revision as of 16:32, 29 March 2012


Name:b cell line:RPMI1788
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stage33 year old adult
sexmale
age33
cell typeb cell
cell lineRPMI1788
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-penis0.0698
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-lymphoma0.518
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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: CNhs10744

Jaspar motifP-value
MA0002.20.0483
MA0003.10.763
MA0004.10.0144
MA0006.10.128
MA0007.10.282
MA0009.10.433
MA0014.10.723
MA0017.10.224
MA0018.20.198
MA0019.10.244
MA0024.11.83346e-5
MA0025.10.62
MA0027.10.677
MA0028.11.12908e-4
MA0029.10.439
MA0030.10.0456
MA0031.10.217
MA0035.20.958
MA0038.10.486
MA0039.20.982
MA0040.10.107
MA0041.10.126
MA0042.10.191
MA0043.10.253
MA0046.10.451
MA0047.20.715
MA0048.10.727
MA0050.13.54772e-17
MA0051.11.3389e-12
MA0052.10.774
MA0055.10.0213
MA0057.10.662
MA0058.10.00577
MA0059.17.23737e-4
MA0060.11.74675e-6
MA0061.12.47067e-14
MA0062.27.17017e-9
MA0065.20.0658
MA0066.10.707
MA0067.10.271
MA0068.10.192
MA0069.10.462
MA0070.10.847
MA0071.10.95
MA0072.10.588
MA0073.10.598
MA0074.10.817
MA0076.12.04537e-6
MA0077.10.244
MA0078.10.0532
MA0079.20.449
MA0080.21.54975e-5
MA0081.10.0189
MA0083.10.28
MA0084.10.211
MA0087.10.244
MA0088.10.0132
MA0090.16.04225e-6
MA0091.10.456
MA0092.10.515
MA0093.10.0148
MA0099.20.15
MA0100.10.122
MA0101.15.05901e-12
MA0102.20.315
MA0103.10.00387
MA0104.23.0351e-4
MA0105.18.42049e-12
MA0106.10.111
MA0107.14.79905e-13
MA0108.20.014
MA0111.10.902
MA0112.20.592
MA0113.10.912
MA0114.10.0692
MA0115.10.828
MA0116.10.00141
MA0117.10.529
MA0119.10.891
MA0122.10.912
MA0124.10.18
MA0125.10.463
MA0131.10.0702
MA0135.10.102
MA0136.14.92883e-9
MA0137.20.688
MA0138.20.229
MA0139.10.465
MA0140.10.572
MA0141.10.531
MA0142.10.317
MA0143.10.524
MA0144.10.246
MA0145.10.451
MA0146.10.333
MA0147.11.34952e-4
MA0148.10.415
MA0149.10.525
MA0150.10.358
MA0152.10.101
MA0153.10.194
MA0154.12.81547e-4
MA0155.10.616
MA0156.16.60216e-8
MA0157.10.152
MA0159.10.166
MA0160.10.129
MA0162.10.806
MA0163.13.64874e-11
MA0164.10.394
MA0258.10.408
MA0259.10.00859



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: CNhs10744

Novel motifP-value
10.0136
100.0218
1000.333
1010.296
1020.765
1030.528
1040.501
1050.735
1060.857
1070.698
1080.458
1090.076
110.234
1100.204
1110.171
1120.501
1130.56
1140.687
1150.956
1160.854
1170.0263
1180.0605
1190.0908
120.996
1200.929
1210.407
1220.599
1232.36055e-4
1240.152
1250.529
1260.176
1270.316
1280.613
1290.809
130.0389
1300.88
1310.793
1320.301
1330.759
1340.789
1350.748
1360.536
1370.604
1380.433
1390.898
140.57
1400.444
1410.449
1420.837
1430.501
1440.289
1450.309
1460.851
1470.104
1480.0547
1490.26
150.132
1500.731
1510.451
1520.146
1530.534
1540.991
1550.0672
1560.956
1570.162
1580.144
1590.748
160.633
1600.387
1610.118
1620.274
1630.887
1640.146
1650.428
1660.518
1670.308
1680.674
1690.815
170.886
180.71
190.492
20.283
200.127
210.28
220.867
230.209
240.134
250.133
260.128
270.904
280.419
290.00662
30.124
300.0712
310.63
320.188
330.275
340.647
350.161
360.0351
370.236
380.643
390.386
40.615
400.347
410.656
420.083
430.49
440.485
450.355
460.283
470.0623
480.0921
490.194
50.864
500.817
510.735
520.606
530.381
540.764
550.208
560.867
570.352
580.128
590.452
60.811
600.672
610.0914
620.189
630.836
640.428
650.843
660.044
670.854
680.3
690.74
70.127
700.796
710.0648
720.269
730.978
740.843
750.00834
760.204
770.419
780.0993
790.64
80.697
800.249
810.183
820.602
830.953
840.26
850.434
860.115
870.142
880.784
890.556
90.472
900.0514
910.746
920.994
930.76
940.402
950.039
960.378
970.252
980.398
990.185



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: CNhs10744


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)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

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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