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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000087,UBERON:0000091,UBERON:0000178,UBERON:0000179,UBERON:0000358,UBERON:0000463,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000478,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001009,UBERON:0001062,UBERON:0002050,UBERON:0002193,UBERON:0002331,UBERON:0002390,UBERON:0002532,UBERON:0003081,UBERON:0004120,UBERON:0004535,UBERON:0005423,UBERON:0005728,UBERON:0007806,UBERON:0008780
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000087,UBERON:0000091,UBERON:0000178,UBERON:0000179,UBERON:0000358,UBERON:0000463,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000478,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001009,UBERON:0001062,UBERON:0002050,UBERON:0002193,UBERON:0002331,UBERON:0002390,UBERON:0002532,UBERON:0003081,UBERON:0004120,UBERON:0004535,UBERON:0005423,UBERON:0005728,UBERON:0007806,UBERON:0008780
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000144,CL:0000255,CL:0000548,CL:0000988,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000144,CL:0000255,CL:0000548,CL:0000988,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101035
|fonse_cell_line=FF:0101035
|fonse_cell_line_closure=FF:0101035
|fonse_cell_line_closure=FF:0101035

Revision as of 16:37, 29 March 2012


Name:cord blood derived cell line:COBL-a untreated
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
sexNA
ageNA
cell typeunclassifiable
cell lineCOBL-a
companyNA
collaborationChieko Kai (University of Tokyo)
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-penis0.00563
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-lymphoma0.577
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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
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: CNhs11045

Jaspar motifP-value
MA0002.20.307
MA0003.10.501
MA0004.10.536
MA0006.10.0698
MA0007.10.135
MA0009.10.781
MA0014.10.326
MA0017.10.832
MA0018.26.74228e-5
MA0019.10.874
MA0024.11.33448e-8
MA0025.10.399
MA0027.10.64
MA0028.15.54519e-5
MA0029.10.968
MA0030.10.0523
MA0031.10.0869
MA0035.20.0709
MA0038.10.00342
MA0039.20.144
MA0040.10.0136
MA0041.10.159
MA0042.10.19
MA0043.10.334
MA0046.10.118
MA0047.20.91
MA0048.10.111
MA0050.10.00173
MA0051.10.0138
MA0052.10.013
MA0055.10.0199
MA0057.10.534
MA0058.10.534
MA0059.10.101
MA0060.17.09735e-10
MA0061.17.2313e-14
MA0062.21.22605e-6
MA0065.20.392
MA0066.10.164
MA0067.10.907
MA0068.10.812
MA0069.10.524
MA0070.10.622
MA0071.10.676
MA0072.10.668
MA0073.10.537
MA0074.10.874
MA0076.11.41573e-5
MA0077.10.612
MA0078.10.1
MA0079.20.168
MA0080.20.707
MA0081.10.795
MA0083.10.616
MA0084.10.776
MA0087.10.184
MA0088.10.193
MA0090.13.50421e-5
MA0091.10.00864
MA0092.10.205
MA0093.10.402
MA0099.28.29963e-4
MA0100.10.086
MA0101.15.45375e-18
MA0102.20.707
MA0103.10.236
MA0104.28.24574e-4
MA0105.11.44155e-4
MA0106.10.0541
MA0107.17.32654e-23
MA0108.20.00221
MA0111.10.995
MA0112.20.0352
MA0113.10.0964
MA0114.10.289
MA0115.10.285
MA0116.10.938
MA0117.10.0303
MA0119.10.116
MA0122.10.182
MA0124.10.279
MA0125.10.272
MA0131.10.0576
MA0135.10.0315
MA0136.10.173
MA0137.20.00492
MA0138.20.203
MA0139.10.941
MA0140.10.113
MA0141.10.487
MA0142.10.487
MA0143.10.024
MA0144.10.904
MA0145.10.003
MA0146.10.267
MA0147.10.00106
MA0148.10.961
MA0149.10.245
MA0150.10.157
MA0152.10.135
MA0153.11.43587e-4
MA0154.10.779
MA0155.10.263
MA0156.10.043
MA0157.10.11
MA0159.10.572
MA0160.10.0566
MA0162.10.0334
MA0163.10.21
MA0164.10.834
MA0258.10.283
MA0259.10.0909



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: CNhs11045

Novel motifP-value
10.863
100.11
1000.149
1010.347
1020.794
1030.536
1040.646
1050.647
1060.0324
1070.0578
1080.473
1090.819
110.56
1100.186
1110.381
1120.48
1130.697
1140.41
1150.369
1160.361
1170.448
1180.508
1190.483
120.564
1200.959
1210.786
1220.267
1230.291
1240.229
1250.583
1260.68
1270.831
1280.0192
1290.364
130.199
1300.914
1310.738
1320.342
1330.822
1340.253
1350.954
1360.439
1370.427
1380.149
1390.521
140.767
1400.45
1410.27
1420.92
1430.873
1440.412
1450.534
1460.298
1470.256
1480.241
1490.0059
150.904
1500.434
1510.269
1520.0415
1530.194
1540.852
1550.446
1560.497
1570.927
1580.733
1590.862
160.252
1600.466
1610.515
1620.149
1630.618
1640.581
1650.798
1660.927
1670.21
1680.438
1690.0344
170.32
180.816
190.0296
20.124
200.148
210.038
220.0742
230.0161
240.147
250.536
260.704
270.409
280.662
290.72
30.557
300.0351
310.262
320.0226
330.769
340.276
350.767
360.0605
370.521
380.609
390.177
40.213
400.868
410.304
420.483
430.47
440.887
450.0519
460.627
470.952
480.965
490.69
50.192
500.778
510.606
520.0936
530.81
540.272
557.35814e-4
560.758
570.95
580.816
590.122
60.822
600.201
610.589
620.968
630.409
640.678
650.174
660.057
670.153
680.114
690.0456
70.679
700.114
710.46
720.241
730.0626
740.374
750.843
760.327
770.00438
780.356
790.0246
80.587
800.236
810.602
820.0893
830.149
840.272
850.0203
860.925
870.458
880.449
890.0246
90.217
900.62
910.405
920.235
930.684
940.969
950.625
960.903
970.0368
980.237
990.126



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: CNhs11045


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)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000988 (hematopoietic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000087 (inner cell mass)
0000091 (bilaminar disc)
0000178 (blood)
0000179 (haemolymphatic fluid)
0000358 (blastocyst)
0000463 (organism substance)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000478 (extraembryonic structure)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001009 (circulatory system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002331 (umbilical cord)
0002390 (hematopoietic system)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0005423 (developing anatomical structure)
0005728 (extraembryonic mesoderm)
0007806 (connecting stalk)
0008780 (inner cell mass derived epiblast)

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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