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FF:12177-128I8: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 16:38, 29 March 2012


Name:Whole blood (ribopure), donor090325, donation2
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
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationMatched_genome_OSC(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-ribopure_minelute_cleanup-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-0.0976
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.15
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.15
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-Whole0.54
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: CNhs11076

Jaspar motifP-value
MA0002.28.32238e-11
MA0003.10.0764
MA0004.10.663
MA0006.10.608
MA0007.10.878
MA0009.10.0588
MA0014.10.885
MA0017.10.0743
MA0018.20.0595
MA0019.10.682
MA0024.10.0151
MA0025.10.7
MA0027.10.449
MA0028.10.414
MA0029.10.952
MA0030.10.0346
MA0031.10.00164
MA0035.20.0096
MA0038.10.029
MA0039.20.192
MA0040.10.365
MA0041.10.759
MA0042.10.721
MA0043.10.725
MA0046.10.197
MA0047.20.224
MA0048.10.204
MA0050.12.41576e-7
MA0051.10.00622
MA0052.10.00791
MA0055.10.0576
MA0057.10.932
MA0058.10.711
MA0059.10.765
MA0060.13.25421e-5
MA0061.10.0385
MA0062.21.65965e-5
MA0065.20.0543
MA0066.10.277
MA0067.10.811
MA0068.10.499
MA0069.10.724
MA0070.10.0226
MA0071.10.684
MA0072.10.561
MA0073.10.531
MA0074.10.488
MA0076.10.0985
MA0077.10.129
MA0078.10.886
MA0079.20.776
MA0080.21.17098e-17
MA0081.10.00137
MA0083.10.482
MA0084.10.519
MA0087.10.945
MA0088.10.298
MA0090.10.0126
MA0091.10.286
MA0092.10.919
MA0093.10.577
MA0099.20.423
MA0100.10.951
MA0101.10.811
MA0102.23.7724e-5
MA0103.10.156
MA0104.20.71
MA0105.17.42227e-5
MA0106.10.459
MA0107.10.793
MA0108.21.72271e-6
MA0111.10.222
MA0112.27.871e-4
MA0113.10.88
MA0114.10.375
MA0115.10.539
MA0116.19.13254e-6
MA0117.10.925
MA0119.10.409
MA0122.10.279
MA0124.10.608
MA0125.10.0939
MA0131.10.68
MA0135.10.724
MA0136.13.77253e-25
MA0137.20.101
MA0138.20.599
MA0139.10.174
MA0140.12.64569e-8
MA0141.10.71
MA0142.10.825
MA0143.10.998
MA0144.10.128
MA0145.10.18
MA0146.10.00819
MA0147.10.687
MA0148.10.781
MA0149.10.38
MA0150.10.0291
MA0152.10.111
MA0153.10.0367
MA0154.10.00392
MA0155.10.892
MA0156.12.56221e-19
MA0157.10.00555
MA0159.10.095
MA0160.10.535
MA0162.10.462
MA0163.11.11557e-6
MA0164.10.544
MA0258.10.0133
MA0259.10.349



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: CNhs11076

Novel motifP-value
10.135
100.0567
1000.73
1010.217
1020.989
1030.173
1040.736
1050.15
1060.0437
1070.586
1080.745
1090.106
110.0997
1100.369
1110.153
1120.143
1130.149
1140.0623
1150.457
1160.8
1170.0346
1180.378
1190.289
120.527
1200.812
1210.875
1220.422
1230.0402
1240.0856
1250.164
1260.344
1270.421
1280.0654
1290.649
130.612
1300.601
1310.901
1320.401
1330.541
1340.957
1350.258
1360.99
1370.0227
1380.0459
1390.0294
140.192
1400.259
1410.428
1420.501
1430.00893
1440.764
1450.188
1460.763
1470.143
1480.131
1490.31
150.0577
1500.913
1510.229
1520.488
1530.569
1540.935
1550.27
1560.654
1570.233
1580.249
1590.226
160.455
1600.499
1610.311
1620.529
1630.312
1640.315
1650.0803
1660.847
1670.819
1680.112
1690.0152
170.5
180.414
190.393
20.311
200.628
210.472
220.269
230.154
240.109
250.186
260.237
270.0889
280.499
290.416
30.0548
300.821
310.592
320.662
330.72
340.295
350.178
360.258
370.203
380.348
390.901
40.656
400.349
410.129
420.185
430.146
440.459
450.603
460.124
470.143
480.235
490.123
50.229
500.978
510.393
520.575
530.0957
540.36
550.0453
560.269
570.637
580.0534
590.0794
60.635
600.0878
610.221
620.0201
630.488
640.368
650.22
660.424
670.288
680.662
690.469
70.134
700.0515
710.093
720.186
730.352
740.555
750.102
760.351
770.674
780.294
790.996
80.377
800.00935
810.23
820.0267
830.614
840.291
850.151
860.191
870.658
880.616
890.374
90.279
900.0273
910.292
920.0946
930.359
940.102
950.338
960.131
970.714
980.0692
990.532



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: CNhs11076


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

UBERON: Anatomy
0000061 (anatomical structure)
0000178 (blood)
0000179 (haemolymphatic fluid)
0000463 (organism substance)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0002193 (hemolymphoid system)
0002390 (hematopoietic system)
0004535 (cardiovascular system)
0007023 (adult organism)

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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