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FF:11267-116G7: 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 17:20, 29 March 2012


Name:Endothelial Cells - Vein, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuevein
dev stageinfant
sexmale
ageNeonatal
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 number1684
catalog numberCA200-R10n
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-penis0.283
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-lymphoma0.105
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: CNhs12497

Jaspar motifP-value
MA0002.20.401
MA0003.10.313
MA0004.10.0634
MA0006.10.281
MA0007.10.00168
MA0009.10.307
MA0014.10.551
MA0017.10.259
MA0018.20.0653
MA0019.10.119
MA0024.10.66
MA0025.10.742
MA0027.10.574
MA0028.10.593
MA0029.10.444
MA0030.10.482
MA0031.10.102
MA0035.23.01402e-4
MA0038.10.00656
MA0039.20.16
MA0040.10.43
MA0041.10.249
MA0042.10.533
MA0043.10.0253
MA0046.10.145
MA0047.20.753
MA0048.10.033
MA0050.12.28453e-6
MA0051.10.00646
MA0052.10.472
MA0055.11.83838e-4
MA0057.10.334
MA0058.10.13
MA0059.10.0533
MA0060.18.40453e-7
MA0061.10.503
MA0062.20.447
MA0065.20.106
MA0066.10.376
MA0067.10.478
MA0068.10.0383
MA0069.10.0179
MA0070.10.561
MA0071.10.177
MA0072.10.131
MA0073.10.262
MA0074.10.513
MA0076.10.0459
MA0077.14.60209e-4
MA0078.10.0098
MA0079.20.515
MA0080.29.47403e-4
MA0081.10.213
MA0083.10.0535
MA0084.10.696
MA0087.10.427
MA0088.10.179
MA0090.10.261
MA0091.10.751
MA0092.10.744
MA0093.10.0862
MA0099.27.51307e-18
MA0100.10.93
MA0101.10.897
MA0102.22.13324e-4
MA0103.10.0373
MA0104.20.409
MA0105.10.486
MA0106.18.5011e-4
MA0107.10.981
MA0108.22.47542e-6
MA0111.10.281
MA0112.20.541
MA0113.10.492
MA0114.10.467
MA0115.10.714
MA0116.10.718
MA0117.10.748
MA0119.10.141
MA0122.10.0893
MA0124.10.421
MA0125.10.749
MA0131.10.855
MA0135.10.0642
MA0136.10.0142
MA0137.20.142
MA0138.20.982
MA0139.10.48
MA0140.11.27605e-4
MA0141.10.0769
MA0142.10.0377
MA0143.10.925
MA0144.10.904
MA0145.10.159
MA0146.10.482
MA0147.10.115
MA0148.10.477
MA0149.10.0347
MA0150.10.00298
MA0152.10.742
MA0153.10.68
MA0154.10.819
MA0155.10.127
MA0156.10.00758
MA0157.10.63
MA0159.10.938
MA0160.10.253
MA0162.10.074
MA0163.10.309
MA0164.10.409
MA0258.10.381
MA0259.10.255



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: CNhs12497

Novel motifP-value
10.916
100.323
1000.169
1010.15
1020.619
1030.991
1040.717
1050.548
1060.837
1070.221
1080.895
1090.0281
110.119
1100.0232
1110.711
1120.252
1130.485
1140.57
1150.919
1160.799
1170.3
1180.894
1190.669
120.073
1200.0446
1210.997
1220.522
1230.0147
1240.419
1250.615
1260.422
1270.512
1280.921
1290.597
130.153
1300.105
1310.551
1320.479
1330.33
1340.535
1350.188
1360.129
1370.294
1380.913
1390.661
140.532
1400.435
1410.627
1420.978
1430.156
1440.213
1450.238
1460.0974
1470.185
1480.135
1490.391
150.725
1500.053
1510.841
1520.103
1530.1
1540.0926
1550.926
1560.439
1570.369
1580.451
1590.819
160.946
1600.0952
1610.411
1620.737
1630.383
1640.866
1650.658
1660.0973
1670.374
1680.721
1690.12
170.048
180.826
190.817
20.993
200.664
210.169
220.155
230.901
240.903
250.551
260.519
270.651
280.0131
290.797
30.933
300.859
310.933
320.211
330.242
340.032
350.936
360.048
370.456
380.208
390.879
40.214
400.00905
410.0696
420.537
430.846
440.0639
450.313
460.432
470.511
480.0702
490.965
50.753
500.971
510.752
520.661
530.218
540.788
550.237
560.914
570.205
580.0651
590.207
60.52
600.963
610.901
620.284
630.823
640.726
650.61
660.0229
670.948
680.507
690.748
70.336
700.655
710.925
720.294
730.00195
740.617
750.491
760.453
770.524
780.901
790.595
80.0298
800.485
810.405
820.108
830.601
840.43
850.227
860.598
870.0417
880.942
890.965
90.146
900.195
910.193
920.676
930.672
940.627
950.0233
960.235
970.604
980.106
990.133



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: CNhs12497


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)
0002543 (vein endothelial cell)
0002546 (embryonic blood vessel endothelial progenitor cell)

UBERON: Anatomy
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000487 (simple squamous epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001009 (circulatory system)
0001062 (anatomical entity)
0001638 (vein)
0001981 (blood vessel)
0001986 (endothelium)
0002049 (vasculature)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003914 (epithelial tube)
0003920 (venous blood vessel)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004582 (venous system)
0004638 (blood vessel endothelium)
0004852 (cardiovascular system endothelium)
0004872 (splanchnic layer of lateral plate mesoderm)
0005423 (developing anatomical structure)
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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