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FF:10206-103F8: 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 - pulmonic 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
sex26
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 numberR1234135-10
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-penis1.208
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-0.382
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs12856

Jaspar motifP-value
MA0002.20.00576
MA0003.10.869
MA0004.19.56141e-4
MA0006.10.804
MA0007.10.209
MA0009.10.333
MA0014.10.155
MA0017.10.608
MA0018.20.0715
MA0019.10.748
MA0024.10.00361
MA0025.10.874
MA0027.10.734
MA0028.11.53077e-7
MA0029.10.826
MA0030.10.747
MA0031.10.977
MA0035.20.413
MA0038.10.00768
MA0039.20.0378
MA0040.10.199
MA0041.10.964
MA0042.10.673
MA0043.10.0134
MA0046.10.0141
MA0047.20.597
MA0048.10.183
MA0050.10.121
MA0051.10.053
MA0052.13.92143e-32
MA0055.10.00114
MA0057.10.808
MA0058.11.19296e-4
MA0059.11.73276e-5
MA0060.14.17226e-8
MA0061.11.47252e-6
MA0062.21.56365e-14
MA0065.20.362
MA0066.10.184
MA0067.10.133
MA0068.10.879
MA0069.10.883
MA0070.10.825
MA0071.10.643
MA0072.10.395
MA0073.10.664
MA0074.10.795
MA0076.11.09282e-9
MA0077.10.917
MA0078.10.521
MA0079.20.67
MA0080.22.28277e-7
MA0081.10.0106
MA0083.13.37424e-6
MA0084.10.884
MA0087.10.888
MA0088.10.0287
MA0090.10.0117
MA0091.10.431
MA0092.10.331
MA0093.14.0146e-4
MA0099.23.29489e-28
MA0100.10.0193
MA0101.16.30421e-5
MA0102.20.0314
MA0103.10.00834
MA0104.21.84993e-5
MA0105.13.20637e-8
MA0106.10.0462
MA0107.12.1527e-6
MA0108.24.16679e-4
MA0111.10.578
MA0112.20.612
MA0113.10.102
MA0114.10.436
MA0115.10.393
MA0116.17.0597e-4
MA0117.10.403
MA0119.10.302
MA0122.10.237
MA0124.10.53
MA0125.10.717
MA0131.10.25
MA0135.10.861
MA0136.11.0032e-13
MA0137.20.631
MA0138.20.451
MA0139.10.0775
MA0140.10.821
MA0141.10.0539
MA0142.10.00451
MA0143.10.326
MA0144.10.455
MA0145.10.458
MA0146.10.138
MA0147.15.97649e-6
MA0148.10.851
MA0149.10.19
MA0150.11.11163e-7
MA0152.10.399
MA0153.10.454
MA0154.10.0886
MA0155.10.866
MA0156.19.61262e-15
MA0157.10.359
MA0159.10.54
MA0160.10.138
MA0162.10.556
MA0163.11.11942e-5
MA0164.10.488
MA0258.10.633
MA0259.10.0237



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: CNhs12856

Novel motifP-value
10.17
100.126
1000.514
1010.246
1020.269
1030.115
1040.098
1050.775
1060.596
1070.487
1080.42
1090.00622
110.072
1100.143
1110.293
1120.826
1130.245
1140.58
1150.724
1160.564
1170.00823
1180.0121
1190.385
120.627
1200.13
1210.424
1220.0343
1230.927
1240.626
1250.566
1260.403
1270.539
1280.459
1290.64
130.119
1300.421
1310.216
1320.0188
1330.298
1340.346
1350.247
1362.99251e-4
1370.441
1380.693
1390.629
140.762
1400.602
1410.919
1420.851
1430.0171
1440.511
1450.359
1460.266
1470.0271
1480.848
1490.377
150.17
1500.362
1510.999
1520.503
1530.126
1540.766
1550.413
1560.831
1570.42
1580.395
1590.142
160.116
1600.865
1610.688
1620.898
1630.377
1640.0597
1650.465
1660.0563
1670.213
1680.823
1690.232
170.402
180.0668
190.289
20.203
200.0664
210.606
220.901
230.428
240.0462
250.258
260.0157
270.39
280.638
291.2163e-4
30.146
300.247
310.894
320.364
330.0469
340.275
350.671
360.0581
370.207
380.542
390.313
40.685
400.0127
410.15
420.213
430.13
440.499
450.48
460.319
470.0888
480.0817
490.736
50.552
500.977
510.424
520.274
530.832
540.727
550.729
560.556
570.298
580.477
590.503
60.962
600.984
610.0742
620.467
630.614
640.146
650.982
664.26348e-4
670.564
680.187
690.62
70.36
700.131
710.0187
720.456
730.0611
740.473
750.0182
760.112
770.62
780.509
790.381
80.251
800.526
810.891
820.416
830.206
840.439
850.2
860.696
872.34822e-6
880.984
890.486
90.857
900.0919
910.0684
920.653
930.713
940.109
952.53242e-4
960.389
970.809
980.748
990.256



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: CNhs12856


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)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000946 (cardial valve)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002146 (pulmonary valve)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0003978 (valve)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0005623 (semi-lunar valve)
0007005 (cardiac mesoderm)
0007023 (adult organism)
0007100 (primary circulatory organ)

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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