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FF:12183-129A5: 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 16:48, 29 March 2012


Name:Whole blood (ribopure), donor090612, 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
sexNA
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)NA
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-0.0787
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
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-Whole0.188
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-Whole0.5
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: CNhs11673

Jaspar motifP-value
MA0002.26.42229e-12
MA0003.10.0395
MA0004.10.554
MA0006.10.704
MA0007.10.61
MA0009.10.0256
MA0014.10.945
MA0017.10.0459
MA0018.20.205
MA0019.10.874
MA0024.10.0115
MA0025.10.37
MA0027.10.384
MA0028.10.396
MA0029.10.589
MA0030.10.015
MA0031.13.60131e-4
MA0035.22.28497e-4
MA0038.10.0325
MA0039.20.112
MA0040.10.0285
MA0041.10.153
MA0042.10.0455
MA0043.10.163
MA0046.10.25
MA0047.20.221
MA0048.10.127
MA0050.11.60079e-6
MA0051.10.0127
MA0052.10.044
MA0055.10.0469
MA0057.10.862
MA0058.10.661
MA0059.10.716
MA0060.18.41243e-4
MA0061.10.0131
MA0062.21.53221e-5
MA0065.20.138
MA0066.10.209
MA0067.10.756
MA0068.10.544
MA0069.10.692
MA0070.10.0126
MA0071.10.573
MA0072.10.677
MA0073.10.442
MA0074.10.737
MA0076.10.0926
MA0077.10.0658
MA0078.10.911
MA0079.20.895
MA0080.21.85501e-17
MA0081.10.00127
MA0083.10.985
MA0084.10.989
MA0087.10.983
MA0088.10.309
MA0090.10.0189
MA0091.10.33
MA0092.10.803
MA0093.10.466
MA0099.20.491
MA0100.10.992
MA0101.10.409
MA0102.22.83248e-5
MA0103.10.202
MA0104.20.702
MA0105.18.72667e-5
MA0106.10.484
MA0107.10.436
MA0108.25.13483e-5
MA0111.10.265
MA0112.20.00124
MA0113.10.904
MA0114.10.448
MA0115.10.455
MA0116.12.57192e-6
MA0117.10.985
MA0119.10.569
MA0122.10.36
MA0124.10.677
MA0125.10.044
MA0131.10.499
MA0135.10.594
MA0136.12.5891e-25
MA0137.20.033
MA0138.20.849
MA0139.10.184
MA0140.11.99468e-14
MA0141.10.593
MA0142.10.961
MA0143.10.587
MA0144.10.0423
MA0145.10.106
MA0146.10.0065
MA0147.10.652
MA0148.10.531
MA0149.10.383
MA0150.10.00143
MA0152.10.168
MA0153.10.035
MA0154.10.00206
MA0155.10.805
MA0156.11.12258e-18
MA0157.10.00618
MA0159.10.198
MA0160.10.565
MA0162.10.438
MA0163.19.24626e-6
MA0164.10.49
MA0258.10.0267
MA0259.10.35



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: CNhs11673

Novel motifP-value
10.177
100.083
1000.511
1010.291
1020.615
1030.14
1040.713
1050.0964
1060.0627
1070.902
1080.79
1090.109
110.0918
1100.285
1110.258
1120.176
1130.174
1140.0437
1150.144
1160.943
1170.0575
1180.367
1190.547
120.439
1200.513
1210.899
1220.282
1230.297
1240.0932
1250.148
1260.184
1270.27
1280.0798
1290.58
130.784
1300.81
1310.686
1320.554
1330.807
1340.811
1350.195
1360.887
1370.00773
1380.051
1390.0119
140.166
1400.647
1410.475
1420.942
1430.00256
1440.521
1450.421
1460.827
1470.154
1480.261
1490.507
150.0378
1500.98
1510.286
1520.354
1530.487
1540.931
1550.239
1560.834
1570.343
1580.13
1590.424
160.464
1600.659
1610.372
1620.535
1630.407
1640.331
1650.0841
1660.836
1670.709
1680.163
1690.0203
170.412
180.414
190.344
20.204
200.614
210.514
220.165
230.0621
240.0567
250.166
260.319
270.0817
280.408
290.493
30.104
300.976
310.485
320.795
330.565
340.234
350.193
360.448
370.172
380.251
390.902
40.939
400.422
410.0476
420.218
430.131
440.561
450.442
460.139
470.182
480.258
490.137
50.196
500.888
510.401
520.524
530.158
540.293
550.113
560.24
570.796
580.0421
590.0718
60.663
600.0604
610.231
620.0104
630.598
640.333
650.136
660.601
670.298
680.51
690.571
70.153
700.0239
710.111
720.201
730.297
740.504
750.0985
760.449
770.64
780.315
790.942
80.572
800.00578
810.342
820.0251
830.828
840.568
850.164
860.156
870.678
880.581
890.299
90.207
900.0479
910.265
920.0748
930.107
940.149
950.517
960.0876
970.787
980.0679
990.259



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: CNhs11673


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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