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FF:10207-103F9: 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 17:26, 29 March 2012


Name:heart - tricuspid valve, 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
sex77
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 numberR1234136-10
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-penis1.13
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-0.362
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: CNhs12857

Jaspar motifP-value
MA0002.20.00454
MA0003.10.574
MA0004.10.111
MA0006.10.922
MA0007.10.682
MA0009.10.218
MA0014.10.0958
MA0017.10.333
MA0018.20.247
MA0019.10.949
MA0024.10.00222
MA0025.10.147
MA0027.10.916
MA0028.18.74207e-7
MA0029.10.981
MA0030.10.786
MA0031.10.844
MA0035.20.606
MA0038.10.00848
MA0039.20.00614
MA0040.10.517
MA0041.10.54
MA0042.10.851
MA0043.10.701
MA0046.10.0558
MA0047.20.634
MA0048.10.543
MA0050.10.731
MA0051.10.875
MA0052.18.02048e-8
MA0055.10.153
MA0057.10.72
MA0058.10.0143
MA0059.10.124
MA0060.12.93549e-8
MA0061.10.481
MA0062.21.70683e-11
MA0065.20.0308
MA0066.10.156
MA0067.10.791
MA0068.10.124
MA0069.10.506
MA0070.10.293
MA0071.10.298
MA0072.10.229
MA0073.10.967
MA0074.10.97
MA0076.11.44707e-10
MA0077.10.374
MA0078.10.8
MA0079.20.556
MA0080.20.00924
MA0081.10.117
MA0083.10.00755
MA0084.10.388
MA0087.10.339
MA0088.10.0424
MA0090.10.00308
MA0091.10.451
MA0092.10.208
MA0093.10.053
MA0099.29.34849e-10
MA0100.10.0146
MA0101.10.301
MA0102.20.0437
MA0103.15.79785e-4
MA0104.20.146
MA0105.10.0228
MA0106.10.912
MA0107.10.131
MA0108.24.93993e-14
MA0111.10.393
MA0112.20.23
MA0113.10.0169
MA0114.10.0488
MA0115.10.556
MA0116.10.00478
MA0117.10.836
MA0119.10.199
MA0122.10.523
MA0124.10.584
MA0125.10.174
MA0131.10.722
MA0135.10.111
MA0136.16.81433e-4
MA0137.21.74782e-5
MA0138.20.479
MA0139.11.97769e-4
MA0140.10.338
MA0141.10.661
MA0142.10.0408
MA0143.10.558
MA0144.10.00687
MA0145.10.66
MA0146.10.0675
MA0147.10.324
MA0148.10.782
MA0149.10.588
MA0150.10.0831
MA0152.10.116
MA0153.10.256
MA0154.10.267
MA0155.10.396
MA0156.11.14343e-5
MA0157.10.514
MA0159.10.302
MA0160.10.871
MA0162.10.206
MA0163.10.00158
MA0164.10.974
MA0258.10.599
MA0259.10.539



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: CNhs12857

Novel motifP-value
10.39
100.23
1000.946
1010.806
1020.207
1030.00856
1040.465
1050.379
1060.155
1070.043
1080.0566
1090.00601
110.216
1100.185
1110.732
1120.542
1130.0158
1140.855
1150.17
1160.912
1170.0331
1180.0607
1190.192
120.741
1200.0853
1210.256
1220.194
1230.035
1240.461
1250.609
1260.998
1270.0658
1280.141
1290.412
130.538
1300.286
1310.225
1320.183
1330.27
1340.485
1350.938
1360.0308
1370.396
1380.724
1390.127
140.76
1400.0584
1410.65
1420.704
1430.106
1440.879
1450.339
1460.759
1470.207
1480.861
1490.598
150.278
1500.806
1510.775
1520.909
1530.0479
1540.782
1550.363
1560.463
1570.406
1580.294
1590.4
160.0104
1600.445
1610.0558
1620.946
1630.87
1640.478
1650.0919
1660.581
1670.783
1680.642
1690.308
170.678
180.103
190.902
20.726
200.946
210.538
220.715
230.104
240.0154
250.116
260.721
270.0381
280.998
295.29635e-4
30.378
300.671
310.704
320.0161
330.129
340.365
350.859
360.18
370.249
380.66
390.0723
40.313
400.00583
410.414
420.759
430.579
440.196
450.79
460.633
470.0134
480.135
490.734
50.663
500.278
510.588
520.137
530.289
540.649
550.933
560.41
570.878
580.473
590.0889
60.289
600.468
610.11
620.464
630.471
640.148
650.645
660.0206
670.485
680.378
690.338
70.391
700.356
710.0875
720.709
730.361
740.73
750.0378
760.689
770.655
780.947
790.87
80.209
800.884
810.476
820.88
830.996
840.71
850.088
860.651
872.22422e-5
880.555
890.264
90.995
900.699
910.201
920.297
930.327
940.361
952.93808e-4
960.314
970.574
980.909
990.719



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: CNhs12857


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)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0000946 (cardial valve)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002062 (endocardial cushion)
0002078 (right cardiac atrium)
0002081 (cardiac atrium)
0002133 (atrioventricular valve)
0002134 (tricuspid valve)
0002165 (endocardium)
0002342 (neural crest)
0002346 (neurectoderm)
0002523 (tunica intima)
0002532 (epiblast (generic))
0003075 (neural plate)
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0003978 (valve)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004145 (outflow tract)
0004151 (cardiac chamber)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004872 (splanchnic layer of lateral plate mesoderm)
0004923 (organ component layer)
0005208 (right atrium valve)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0005946 (outflow tract of atrium)
0005965 (outflow part of right atrium)
0005983 (heart layer)
0006598 (presumptive structure)
0006965 (vascular cord)
0007005 (cardiac mesoderm)
0007023 (adult organism)
0007100 (primary circulatory organ)
0007284 (presumptive neural plate)
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

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