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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002193,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002193,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423
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|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:0002092,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100583
|fonse_cell_line=FF:0100583
|fonse_cell_line_closure=FF:0100583
|fonse_cell_line_closure=FF:0100583

Revision as of 16:41, 29 March 2012


Name:myeloma cell line:PCM6
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 stageNA
sexfemale
age60
cell typeb cell
cell linePCM6
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-penis-0.0772
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-lymphoma0.0601
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs11258

Jaspar motifP-value
MA0002.20.00986
MA0003.10.559
MA0004.10.103
MA0006.10.407
MA0007.10.936
MA0009.10.747
MA0014.10.818
MA0017.10.116
MA0018.20.118
MA0019.10.06
MA0024.10.606
MA0025.10.591
MA0027.10.673
MA0028.13.8864e-7
MA0029.10.116
MA0030.10.0933
MA0031.10.173
MA0035.20.896
MA0038.10.0279
MA0039.20.836
MA0040.10.482
MA0041.10.279
MA0042.10.809
MA0043.10.547
MA0046.10.659
MA0047.20.916
MA0048.10.593
MA0050.12.93597e-23
MA0051.11.21924e-14
MA0052.10.148
MA0055.10.517
MA0057.10.958
MA0058.10.049
MA0059.10.0032
MA0060.10.0395
MA0061.10.0189
MA0062.28.08783e-12
MA0065.20.0137
MA0066.10.507
MA0067.10.978
MA0068.10.131
MA0069.10.986
MA0070.10.9
MA0071.10.701
MA0072.10.843
MA0073.10.719
MA0074.10.778
MA0076.15.37819e-11
MA0077.10.0329
MA0078.10.25
MA0079.20.372
MA0080.21.13978e-5
MA0081.10.0026
MA0083.10.0809
MA0084.10.571
MA0087.10.0606
MA0088.10.0162
MA0090.19.28571e-5
MA0091.10.576
MA0092.10.965
MA0093.10.109
MA0099.20.217
MA0100.10.208
MA0101.10.231
MA0102.20.334
MA0103.10.02
MA0104.20.00548
MA0105.11.18891e-5
MA0106.10.761
MA0107.10.104
MA0108.22.1794e-19
MA0111.10.468
MA0112.20.0455
MA0113.10.471
MA0114.10.0109
MA0115.10.123
MA0116.14.42599e-5
MA0117.10.596
MA0119.10.422
MA0122.10.497
MA0124.10.129
MA0125.10.534
MA0131.10.0919
MA0135.11.49875e-4
MA0136.15.2634e-8
MA0137.20.381
MA0138.20.835
MA0139.10.0787
MA0140.10.475
MA0141.10.234
MA0142.10.115
MA0143.10.772
MA0144.10.949
MA0145.10.645
MA0146.10.0319
MA0147.10.00919
MA0148.10.261
MA0149.10.162
MA0150.10.106
MA0152.10.174
MA0153.10.0886
MA0154.10.032
MA0155.10.54
MA0156.14.29527e-10
MA0157.10.941
MA0159.10.00602
MA0160.10.181
MA0162.10.461
MA0163.11.52959e-11
MA0164.10.903
MA0258.10.152
MA0259.10.129



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: CNhs11258

Novel motifP-value
10.00985
100.00996
1000.504
1010.207
1020.538
1030.0551
1040.558
1050.986
1060.476
1070.294
1080.526
1090.045
110.108
1100.196
1110.0305
1120.121
1130.864
1140.268
1150.242
1160.763
1170.00123
1180.377
1190.105
120.863
1200.254
1210.719
1220.722
1230.00548
1240.426
1250.592
1260.189
1270.968
1280.298
1290.316
130.0983
1300.838
1310.238
1320.293
1330.211
1340.779
1350.0931
1360.235
1370.443
1380.238
1390.574
140.599
1400.128
1410.208
1420.656
1430.506
1440.985
1450.588
1460.986
1470.212
1480.0194
1490.922
150.338
1500.353
1510.916
1520.926
1530.798
1540.865
1550.0521
1560.148
1570.393
1580.321
1590.594
160.419
1600.542
1610.0457
1620.29
1630.362
1640.115
1650.347
1660.612
1670.205
1680.709
1690.0575
170.565
180.0221
190.888
20.463
200.346
210.588
220.75
230.629
240.383
250.0899
260.085
270.444
280.624
290.101
30.154
300.0772
310.79
320.775
330.269
340.36
350.436
360.0323
370.0632
380.482
390.697
40.959
400.431
410.918
420.269
430.253
440.0356
450.483
460.145
470.0336
480.0779
490.271
50.476
500.603
510.602
520.139
530.945
540.692
550.974
560.897
570.161
580.175
590.977
60.658
600.636
610.165
620.165
630.592
640.213
650.722
660.176
670.632
680.0483
690.837
70.0999
700.143
710.0319
720.0839
730.125
740.568
750.00157
760.269
770.654
780.0651
790.366
80.187
800.969
810.0212
820.283
830.818
840.994
850.345
860.328
870.192
880.868
890.68
90.7
900.0112
910.969
920.411
930.725
940.0151
950.028
960.138
970.373
980.328
990.202



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: CNhs11258


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)
0002092 (bone marrow cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060083 (immune system cancer)
0070004 (myeloma)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic cancer)
4 (disease)
4960 (bone marrow cancer)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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