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FF:10191-103E2: 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 17:25, 29 March 2012


Name:vein, adult
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sex24
ageM
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyBiochain
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberR1234020-10
sample typeNA
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-0.067
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-lymphoma-0.0753
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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-Whole0.0796
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: CNhs12844

Jaspar motifP-value
MA0002.20.0898
MA0003.10.0183
MA0004.10.135
MA0006.10.271
MA0007.10.996
MA0009.10.678
MA0014.10.124
MA0017.10.315
MA0018.20.0741
MA0019.10.0119
MA0024.10.307
MA0025.10.985
MA0027.10.817
MA0028.11.49695e-4
MA0029.10.964
MA0030.10.25
MA0031.10.417
MA0035.20.865
MA0038.10.0379
MA0039.20.669
MA0040.10.917
MA0041.10.399
MA0042.10.413
MA0043.10.00656
MA0046.10.271
MA0047.20.921
MA0048.10.00164
MA0050.14.39942e-6
MA0051.10.0211
MA0052.12.46706e-8
MA0055.12.07599e-6
MA0057.10.544
MA0058.10.0491
MA0059.10.00504
MA0060.10.0141
MA0061.10.193
MA0062.20.00918
MA0065.20.861
MA0066.10.674
MA0067.10.0991
MA0068.10.00254
MA0069.10.773
MA0070.10.437
MA0071.10.274
MA0072.10.212
MA0073.10.643
MA0074.10.496
MA0076.10.00136
MA0077.10.48
MA0078.10.543
MA0079.20.0545
MA0080.24.53145e-10
MA0081.10.0652
MA0083.10.0143
MA0084.10.762
MA0087.10.427
MA0088.10.016
MA0090.10.77
MA0091.10.272
MA0092.10.439
MA0093.10.101
MA0099.21.54515e-27
MA0100.10.359
MA0101.10.0956
MA0102.20.394
MA0103.10.166
MA0104.20.00331
MA0105.10.0335
MA0106.10.0294
MA0107.10.154
MA0108.21.17389e-15
MA0111.10.832
MA0112.20.773
MA0113.10.199
MA0114.10.575
MA0115.10.89
MA0116.10.412
MA0117.10.154
MA0119.10.47
MA0122.10.0447
MA0124.10.555
MA0125.10.954
MA0131.10.229
MA0135.10.269
MA0136.15.84143e-6
MA0137.20.21
MA0138.20.0194
MA0139.10.431
MA0140.10.16
MA0141.10.0595
MA0142.10.265
MA0143.10.272
MA0144.10.292
MA0145.10.303
MA0146.10.675
MA0147.10.0043
MA0148.10.29
MA0149.10.0736
MA0150.13.13009e-8
MA0152.10.461
MA0153.10.84
MA0154.10.247
MA0155.10.0262
MA0156.10.00661
MA0157.10.76
MA0159.10.648
MA0160.10.196
MA0162.10.604
MA0163.10.102
MA0164.10.453
MA0258.10.736
MA0259.10.0242



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: CNhs12844

Novel motifP-value
10.154
100.109
1000.0544
1010.694
1020.499
1030.91
1040.745
1050.838
1060.297
1070.0402
1080.58
1090.285
110.553
1100.325
1110.461
1120.345
1130.0534
1140.151
1150.19
1160.727
1170.0706
1180.0171
1190.749
120.933
1200.151
1210.571
1220.775
1230.0905
1240.456
1250.353
1260.998
1270.402
1280.198
1290.464
130.00869
1300.682
1310.658
1320.0616
1330.00605
1340.0448
1350.00729
1360.913
1370.581
1380.62
1390.506
140.826
1400.779
1410.485
1420.186
1430.894
1440.896
1450.796
1460.187
1470.854
1480.557
1490.369
150.129
1500.821
1510.727
1520.151
1530.504
1540.288
1550.638
1560.418
1570.384
1580.282
1590.784
160.879
1600.377
1610.306
1620.866
1630.0726
1640.0169
1650.741
1660.194
1670.0143
1680.0447
1690.476
170.85
180.133
190.356
20.00336
200.00398
210.808
220.621
230.394
240.558
250.927
260.379
270.0302
280.544
290.112
30.422
300.0385
310.873
320.728
330.237
340.0597
350.835
360.0663
370.391
380.986
390.44
40.48
400.184
410.249
420.409
430.773
440.232
450.121
460.729
470.428
480.525
490.287
50.282
500.38
510.953
520.347
530.703
540.838
550.785
560.897
570.0991
580.541
590.189
60.414
600.402
610.902
620.673
630.945
640.517
650.547
660.00731
670.506
680.417
690.801
70.899
700.174
710.137
720.167
730.613
740.642
750.0884
760.0292
770.124
780.566
790.22
80.834
808.99381e-4
810.622
820.443
830.739
840.271
850.433
860.375
870.64
880.722
890.613
90.0943
900.0889
910.175
920.617
930.297
940.356
950.192
960.543
970.58
980.59
990.438



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: CNhs12844


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
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001009 (circulatory system)
0001062 (anatomical entity)
0001638 (vein)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003914 (epithelial tube)
0003920 (venous blood vessel)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004582 (venous system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005423 (developing anatomical structure)
0006965 (vascular cord)
0007023 (adult organism)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)

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