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FF:10078-102A6: 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 16:53, 29 March 2012


Name:left ventricle, adult, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueleft ventricle
dev stage73 years old adult
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number5060611
catalog numberCat:AM6856
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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-penis0.607
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-0.368
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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
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: CNhs11789

Jaspar motifP-value
MA0002.20.225
MA0003.10.0275
MA0004.10.00992
MA0006.10.178
MA0007.10.186
MA0009.10.0104
MA0014.10.686
MA0017.10.0401
MA0018.20.0123
MA0019.10.0364
MA0024.10.00443
MA0025.10.194
MA0027.10.787
MA0028.19.11864e-9
MA0029.10.699
MA0030.10.92
MA0031.10.865
MA0035.22.1763e-4
MA0038.10.00107
MA0039.20.214
MA0040.10.83
MA0041.10.151
MA0042.10.355
MA0043.17.83593e-4
MA0046.10.0198
MA0047.20.409
MA0048.10.00195
MA0050.10.022
MA0051.10.195
MA0052.11.57711e-32
MA0055.10.0123
MA0057.10.289
MA0058.18.24544e-4
MA0059.10.0193
MA0060.11.77662e-5
MA0061.10.00864
MA0062.21.40854e-15
MA0065.20.00233
MA0066.10.193
MA0067.10.298
MA0068.10.164
MA0069.10.52
MA0070.10.533
MA0071.10.0395
MA0072.10.81
MA0073.10.877
MA0074.10.477
MA0076.15.49531e-10
MA0077.10.35
MA0078.10.593
MA0079.20.183
MA0080.29.54762e-4
MA0081.10.0275
MA0083.10.0065
MA0084.10.979
MA0087.10.484
MA0088.10.011
MA0090.10.0413
MA0091.10.0786
MA0092.10.057
MA0093.10.00597
MA0099.21.92071e-9
MA0100.10.0336
MA0101.10.0753
MA0102.20.206
MA0103.10.975
MA0104.21.34472e-4
MA0105.10.0199
MA0106.10.168
MA0107.10.0394
MA0108.28.43593e-12
MA0111.10.259
MA0112.20.00107
MA0113.10.00486
MA0114.10.0832
MA0115.10.125
MA0116.10.577
MA0117.10.253
MA0119.10.164
MA0122.10.137
MA0124.10.891
MA0125.10.322
MA0131.10.018
MA0135.10.597
MA0136.11.13825e-8
MA0137.20.655
MA0138.20.128
MA0139.10.405
MA0140.10.0535
MA0141.13.21661e-7
MA0142.10.146
MA0143.10.576
MA0144.10.951
MA0145.10.0443
MA0146.10.766
MA0147.13.42518e-4
MA0148.10.386
MA0149.10.948
MA0150.10.149
MA0152.10.256
MA0153.10.717
MA0154.10.256
MA0155.10.028
MA0156.13.909e-8
MA0157.10.946
MA0159.10.00997
MA0160.12.16462e-4
MA0162.10.154
MA0163.10.09
MA0164.10.714
MA0258.10.00363
MA0259.10.0459



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: CNhs11789

Novel motifP-value
10.701
100.205
1000.962
1010.526
1020.658
1030.827
1040.651
1050.49
1060.0288
1070.0251
1080.323
1090.705
110.443
1100.389
1110.97
1120.203
1130.4
1140.689
1150.164
1160.602
1170.0486
1180.246
1190.0494
120.535
1200.155
1210.571
1220.914
1230.055
1240.749
1250.408
1260.707
1270.485
1280.0911
1290.509
130.451
1300.644
1310.0458
1320.0564
1330.226
1340.165
1350.202
1360.824
1370.584
1380.461
1390.222
140.709
1400.428
1410.37
1420.485
1430.614
1440.55
1450.919
1460.481
1470.0295
1480.223
1490.0443
150.65
1500.514
1510.277
1520.122
1530.287
1540.61
1550.789
1560.214
1570.704
1580.34
1590.308
160.626
1600.164
1610.695
1620.917
1630.631
1640.128
1650.748
1660.0742
1670.38
1680.0891
1690.0317
170.435
180.506
190.0445
20.0773
200.0469
210.78
220.101
230.012
240.0686
250.963
260.426
270.185
280.73
290.0738
30.648
300.15
310.499
320.428
330.994
340.0921
350.739
360.451
370.844
380.541
390.142
40.778
400.456
410.409
420.326
430.61
440.00333
450.144
460.542
470.734
480.584
490.648
50.532
500.828
510.961
520.0434
530.571
540.663
550.829
560.99
570.572
580.773
590.159
60.783
600.062
610.21
620.273
630.578
640.881
650.0841
660.0152
670.551
680.386
690.337
70.78
700.776
710.639
720.495
730.499
740.294
750.172
760.134
770.0819
780.375
790.118
80.329
800.329
810.592
820.17
830.308
840.371
850.00552
860.917
870.319
880.885
890.107
90.348
900.232
910.11
920.115
930.642
940.356
950.223
960.394
970.714
980.111
990.0523



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: CNhs11789


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)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002082 (cardiac ventricle)
0002084 (heart left ventricle)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004151 (cardiac chamber)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
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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