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FF:11243-116E1: 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 16:36, 29 March 2012


Name:Endothelial Cells - Umbilical 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
tissueumbilical vein
dev stagefetus
sexunknown
agefetal
cell typeblood vessel endothelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number4242
catalog numberSC8005
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-0.116
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-lymphoma0.55
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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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: CNhs10872

Jaspar motifP-value
MA0002.21.41488e-5
MA0003.10.199
MA0004.10.613
MA0006.10.456
MA0007.10.917
MA0009.10.947
MA0014.10.666
MA0017.10.168
MA0018.20.00387
MA0019.10.835
MA0024.11.24691e-6
MA0025.10.0414
MA0027.10.866
MA0028.10.156
MA0029.10.846
MA0030.10.386
MA0031.10.705
MA0035.20.228
MA0038.10.0373
MA0039.20.526
MA0040.10.763
MA0041.10.704
MA0042.10.907
MA0043.12.04868e-4
MA0046.10.467
MA0047.20.927
MA0048.10.0234
MA0050.10.489
MA0051.10.0928
MA0052.10.0924
MA0055.10.0243
MA0057.10.605
MA0058.10.896
MA0059.10.55
MA0060.11.52183e-5
MA0061.16.74532e-5
MA0062.20.708
MA0065.20.0794
MA0066.10.24
MA0067.10.204
MA0068.10.0373
MA0069.10.0708
MA0070.10.58
MA0071.10.997
MA0072.10.792
MA0073.10.532
MA0074.10.556
MA0076.10.753
MA0077.13.11727e-4
MA0078.10.197
MA0079.20.866
MA0080.20.0718
MA0081.10.237
MA0083.10.0428
MA0084.10.0208
MA0087.10.0216
MA0088.10.0462
MA0090.10.463
MA0091.10.27
MA0092.10.453
MA0093.10.671
MA0099.20.279
MA0100.10.282
MA0101.10.0691
MA0102.29.81356e-4
MA0103.10.00242
MA0104.20.504
MA0105.19.66229e-4
MA0106.10.0731
MA0107.10.0152
MA0108.20.00178
MA0111.10.368
MA0112.22.05412e-5
MA0113.10.401
MA0114.10.0498
MA0115.10.336
MA0116.10.0233
MA0117.10.546
MA0119.10.268
MA0122.10.356
MA0124.10.171
MA0125.10.795
MA0131.10.0902
MA0135.10.0517
MA0136.10.0544
MA0137.20.778
MA0138.20.259
MA0139.10.579
MA0140.10.266
MA0141.10.445
MA0142.10.318
MA0143.10.833
MA0144.10.894
MA0145.10.171
MA0146.10.0871
MA0147.10.603
MA0148.10.387
MA0149.10.0226
MA0150.10.107
MA0152.10.68
MA0153.10.216
MA0154.10.00666
MA0155.10.745
MA0156.10.0152
MA0157.10.926
MA0159.10.07
MA0160.10.134
MA0162.10.801
MA0163.10.0797
MA0164.10.771
MA0258.10.00229
MA0259.10.592



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: CNhs10872

Novel motifP-value
10.814
100.986
1000.433
1010.925
1020.565
1030.194
1040.807
1050.771
1060.00781
1070.67
1080.453
1090.273
110.506
1100.384
1110.72
1120.183
1130.253
1140.35
1150.305
1160.415
1170.745
1180.951
1190.507
120.508
1200.261
1210.287
1220.221
1230.706
1240.109
1250.575
1260.311
1270.0662
1280.129
1290.824
130.465
1300.474
1310.245
1320.349
1330.478
1340.935
1350.548
1360.0782
1370.204
1380.804
1390.0183
140.526
1400.184
1410.317
1420.0055
1430.0533
1440.703
1450.948
1460.993
1470.778
1480.0455
1490.517
150.204
1500.824
1510.282
1520.35
1530.116
1540.711
1550.183
1560.207
1570.0604
1580.0378
1590.0931
160.281
1600.836
1610.131
1620.931
1630.884
1640.273
1650.523
1660.812
1670.426
1680.71
1690.201
170.201
180.00828
190.474
20.29
200.209
210.476
220.179
230.0155
240.954
250.517
260.181
270.203
280.73
290.79
30.58
300.274
310.156
320.00765
330.728
340.901
350.162
360.238
370.447
380.733
390.541
40.11
400.745
410.839
420.884
430.0813
440.296
450.319
460.102
470.94
480.682
490.104
50.354
500.994
510.296
520.181
530.48
540.253
550.922
560.527
570.701
580.0746
590.167
60.641
600.0378
610.911
620.0803
630.627
640.306
650.0719
660.218
670.966
680.631
690.633
70.928
709.6009e-5
710.268
720.981
730.848
740.645
750.706
760.768
770.116
780.968
790.33
80.905
800.608
810.102
820.139
830.678
840.729
850.00785
860.508
870.63
880.479
890.0322
90.398
900.58
910.495
920.322
930.58
940.0996
950.703
960.366
970.584
980.129
990.176



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: CNhs10872


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)
0002618 (endothelial cell of umbilical vein)

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)
0002066 (umbilical vein)
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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