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FF:11343-117G2: 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 17:04, 29 March 2012


Name:Endothelial Cells - Thoracic, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueinternal thoracic artery
dev stage50 years old adult
sexmale
age50
cell typeblood vessel endothelial cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1555
catalog numberCA308-R10a
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-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-penis-0.0776
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-0.216
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs11978

Jaspar motifP-value
MA0002.20.81
MA0003.10.281
MA0004.10.82
MA0006.10.1
MA0007.10.13
MA0009.10.886
MA0014.10.53
MA0017.10.103
MA0018.26.56659e-5
MA0019.10.0932
MA0024.10.00101
MA0025.10.729
MA0027.10.512
MA0028.10.036
MA0029.10.0765
MA0030.10.141
MA0031.10.148
MA0035.20.0344
MA0038.10.00869
MA0039.20.802
MA0040.10.15
MA0041.10.339
MA0042.10.852
MA0043.13.65745e-6
MA0046.10.695
MA0047.20.168
MA0048.10.488
MA0050.10.00284
MA0051.10.0633
MA0052.10.0184
MA0055.10.405
MA0057.10.178
MA0058.10.693
MA0059.10.285
MA0060.16.34178e-4
MA0061.10.497
MA0062.20.00103
MA0065.20.0317
MA0066.10.255
MA0067.10.0137
MA0068.10.394
MA0069.10.472
MA0070.10.772
MA0071.10.128
MA0072.10.456
MA0073.10.527
MA0074.10.145
MA0076.16.88134e-4
MA0077.12.52042e-6
MA0078.10.0182
MA0079.20.589
MA0080.20.82
MA0081.10.62
MA0083.10.347
MA0084.10.212
MA0087.10.122
MA0088.10.328
MA0090.10.37
MA0091.10.134
MA0092.10.662
MA0093.10.708
MA0099.20.0186
MA0100.10.249
MA0101.10.966
MA0102.23.16776e-5
MA0103.10.574
MA0104.20.302
MA0105.10.122
MA0106.10.00697
MA0107.10.756
MA0108.20.626
MA0111.10.882
MA0112.20.0149
MA0113.10.478
MA0114.10.764
MA0115.10.415
MA0116.10.0267
MA0117.10.214
MA0119.10.0717
MA0122.10.645
MA0124.10.792
MA0125.10.351
MA0131.10.139
MA0135.10.994
MA0136.10.26
MA0137.20.0441
MA0138.20.475
MA0139.10.213
MA0140.10.449
MA0141.10.00692
MA0142.10.568
MA0143.10.476
MA0144.10.881
MA0145.10.121
MA0146.10.179
MA0147.10.741
MA0148.10.0187
MA0149.10.0704
MA0150.10.938
MA0152.10.999
MA0153.10.36
MA0154.10.0761
MA0155.10.0381
MA0156.10.52
MA0157.10.509
MA0159.10.031
MA0160.10.536
MA0162.10.0888
MA0163.10.0577
MA0164.10.3
MA0258.10.0375
MA0259.10.404



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: CNhs11978

Novel motifP-value
10.356
100.95
1000.817
1010.342
1020.502
1030.132
1040.945
1050.305
1060.00961
1070.0298
1080.143
1090.167
110.0522
1100.0556
1110.0654
1120.161
1130.888
1140.117
1150.232
1160.14
1170.567
1180.214
1190.273
120.849
1200.00324
1210.882
1220.264
1230.602
1240.542
1250.291
1260.875
1270.263
1280.233
1290.0789
130.421
1300.617
1310.914
1320.379
1330.59
1340.511
1350.135
1360.749
1370.192
1380.671
1390.0713
140.827
1400.967
1410.39
1420.837
1430.012
1440.822
1450.0814
1460.289
1470.0656
1480.593
1490.0211
150.5
1500.254
1510.303
1520.0325
1530.0517
1540.676
1550.8
1560.158
1570.956
1580.324
1590.965
160.312
1600.00518
1610.634
1620.723
1630.714
1640.159
1650.873
1660.563
1670.648
1680.429
1690.0245
170.103
180.166
190.0606
20.255
200.977
210.751
220.243
230.109
240.738
250.858
260.376
270.201
280.266
290.476
30.517
300.896
310.681
320.0404
330.556
340.254
350.624
360.309
370.0887
380.311
390.213
40.734
400.0702
410.0895
420.884
430.314
440.145
450.3
460.0725
470.188
480.0856
490.433
50.791
500.65
510.311
520.597
530.687
540.49
550.759
560.622
570.233
580.914
590.0079
60.878
600.26
610.8
620.436
630.226
640.362
650.0755
660.983
670.349
680.218
690.133
70.693
700.106
710.368
720.697
730.0163
740.97
750.335
760.896
770.0189
780.544
791.87768e-4
80.029
800.595
810.73
820.185
830.469
840.135
850.085
860.851
870.242
880.891
890.0168
90.262
900.963
910.245
920.198
930.593
940.844
950.145
960.584
970.477
980.625
990.0171



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: CNhs11978


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000071 (blood vessel endothelial cell)
0000076 (squamous epithelial cell)
0000115 (endothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002139 (endothelial cell of vascular tree)
0002321 (embryonic cell)
0002371 (somatic cell)
0002544 (aortic endothelial cell)
0002545 (thoracic aorta endothelial cell)
0002546 (embryonic blood vessel endothelial progenitor cell)
1000413 (endothelial cell of artery)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000487 (simple squamous epithelium)
0000490 (unilaminar epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000947 (aorta)
0001009 (circulatory system)
0001062 (anatomical entity)
0001515 (thoracic aorta)
0001637 (artery)
0001917 (endothelium of artery)
0001981 (blood vessel)
0001986 (endothelium)
0002049 (vasculature)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003509 (arterial blood vessel)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004571 (systemic arterial system)
0004572 (arterial system)
0004573 (systemic artery)
0004638 (blood vessel endothelium)
0004700 (arterial system endothelium)
0004852 (cardiovascular system endothelium)
0004872 (splanchnic layer of lateral plate mesoderm)
0005423 (developing anatomical structure)
0005800 (segment of aorta)
0006914 (squamous epithelium)
0006965 (vascular cord)
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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