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FF:11266-116G6: 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 17:01, 29 March 2012


Name:Endothelial Cells - Thoracic, donor1
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 stage34 years old adult
sexfemale
age34
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 number1696
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-0.129
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-lymphoma0.276
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
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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: CNhs11926

Jaspar motifP-value
MA0002.20.0806
MA0003.10.552
MA0004.10.94
MA0006.10.172
MA0007.10.0636
MA0009.10.409
MA0014.10.484
MA0017.10.447
MA0018.23.33818e-8
MA0019.10.187
MA0024.10.0838
MA0025.10.193
MA0027.10.793
MA0028.10.797
MA0029.10.438
MA0030.10.0382
MA0031.10.321
MA0035.20.0113
MA0038.10.55
MA0039.20.792
MA0040.10.732
MA0041.10.294
MA0042.10.64
MA0043.12.90084e-7
MA0046.10.699
MA0047.20.391
MA0048.10.057
MA0050.10.0117
MA0051.10.575
MA0052.10.2
MA0055.10.00181
MA0057.10.429
MA0058.10.758
MA0059.10.13
MA0060.10.958
MA0061.10.261
MA0062.20.422
MA0065.20.399
MA0066.10.509
MA0067.10.0234
MA0068.10.319
MA0069.10.00607
MA0070.10.63
MA0071.10.269
MA0072.10.471
MA0073.10.44
MA0074.10.412
MA0076.10.0989
MA0077.14.75518e-5
MA0078.10.022
MA0079.20.453
MA0080.20.00243
MA0081.10.235
MA0083.10.0929
MA0084.10.475
MA0087.10.0982
MA0088.10.0201
MA0090.10.491
MA0091.10.874
MA0092.10.381
MA0093.10.917
MA0099.21.39082e-5
MA0100.10.805
MA0101.10.626
MA0102.21.79076e-4
MA0103.10.0274
MA0104.20.597
MA0105.10.29
MA0106.14.43836e-4
MA0107.10.878
MA0108.20.00575
MA0111.10.125
MA0112.20.988
MA0113.10.54
MA0114.10.963
MA0115.10.607
MA0116.10.372
MA0117.10.443
MA0119.10.00765
MA0122.10.193
MA0124.10.313
MA0125.10.776
MA0131.10.335
MA0135.10.151
MA0136.10.00875
MA0137.20.857
MA0138.20.6
MA0139.10.0695
MA0140.10.0106
MA0141.10.131
MA0142.10.748
MA0143.10.411
MA0144.10.162
MA0145.10.487
MA0146.10.816
MA0147.10.192
MA0148.10.116
MA0149.10.0339
MA0150.10.188
MA0152.10.999
MA0153.10.523
MA0154.10.414
MA0155.10.321
MA0156.10.00433
MA0157.10.621
MA0159.10.31
MA0160.10.995
MA0162.10.0546
MA0163.10.0449
MA0164.10.699
MA0258.10.87
MA0259.10.977



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: CNhs11926

Novel motifP-value
10.0344
100.837
1000.148
1010.179
1020.825
1030.224
1040.74
1050.556
1060.704
1070.118
1080.879
1090.0772
110.125
1100.00124
1110.0448
1120.49
1130.672
1140.209
1150.911
1160.282
1170.446
1180.0459
1190.773
120.727
1200.0122
1210.285
1220.527
1230.145
1240.62
1250.949
1260.839
1270.581
1280.422
1290.211
130.341
1300.821
1310.287
1320.314
1330.877
1340.748
1350.414
1360.191
1370.503
1380.699
1390.831
140.135
1400.862
1410.0392
1420.0617
1430.521
1440.298
1450.285
1460.925
1470.387
1480.321
1490.0536
150.652
1500.588
1510.78
1520.0744
1530.273
1540.465
1550.31
1560.187
1570.141
1580.231
1590.29
160.946
1600.0851
1610.496
1620.258
1630.859
1640.225
1650.968
1660.346
1670.463
1680.242
1690.0165
170.381
180.839
190.197
20.922
200.154
210.779
220.651
230.211
240.221
251
260.574
270.556
280.38
290.783
30.76
300.469
310.694
320.422
330.129
340.167
350.427
360.0189
370.175
380.0907
390.237
40.834
400.0149
410.00484
420.202
430.959
440.816
450.863
460.319
470.193
480.144
490.91
50.648
500.947
510.551
520.296
530.753
540.933
550.805
560.676
570.185
580.601
590.358
60.59
600.514
610.654
620.574
630.769
640.916
650.757
660.0625
670.441
680.195
690.938
70.192
700.91
710.458
720.678
730.0117
740.955
750.113
760.563
770.191
780.0916
790.699
80.00713
800.355
810.576
820.64
830.813
840.308
850.746
860.448
870.267
880.856
890.95
90.432
900.476
910.596
920.36
930.769
940.966
950.073
960.173
970.344
980.329
990.00976



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: CNhs11926


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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