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FF:11400-118D5: 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 17:06, 29 March 2012


Name:Endothelial Cells - Umbilical vein, donor3
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 number5025
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-3.111699e-4
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-lymphoma0.463
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
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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: CNhs12010

Jaspar motifP-value
MA0002.26.1228e-5
MA0003.10.43
MA0004.10.594
MA0006.10.771
MA0007.10.627
MA0009.10.673
MA0014.10.915
MA0017.10.185
MA0018.20.116
MA0019.10.0861
MA0024.17.53861e-6
MA0025.10.519
MA0027.10.758
MA0028.10.73
MA0029.10.274
MA0030.10.603
MA0031.10.435
MA0035.20.0238
MA0038.10.00258
MA0039.20.456
MA0040.10.668
MA0041.10.0351
MA0042.10.248
MA0043.10.00191
MA0046.10.384
MA0047.20.689
MA0048.10.163
MA0050.10.626
MA0051.10.0784
MA0052.10.413
MA0055.10.0772
MA0057.10.936
MA0058.10.631
MA0059.10.491
MA0060.12.01319e-12
MA0061.10.00158
MA0062.20.689
MA0065.20.029
MA0066.10.0389
MA0067.10.423
MA0068.10.527
MA0069.10.0464
MA0070.10.373
MA0071.10.694
MA0072.10.589
MA0073.10.876
MA0074.10.469
MA0076.10.654
MA0077.17.31875e-6
MA0078.10.105
MA0079.20.186
MA0080.20.0141
MA0081.10.259
MA0083.10.158
MA0084.10.0979
MA0087.10.0157
MA0088.10.786
MA0090.10.511
MA0091.10.343
MA0092.10.327
MA0093.10.528
MA0099.20.736
MA0100.10.368
MA0101.10.471
MA0102.20.00513
MA0103.10.00178
MA0104.20.653
MA0105.13.55363e-6
MA0106.10.438
MA0107.10.231
MA0108.20.701
MA0111.10.726
MA0112.24.07718e-6
MA0113.10.461
MA0114.10.0555
MA0115.10.996
MA0116.10.0011
MA0117.10.551
MA0119.10.761
MA0122.10.173
MA0124.10.158
MA0125.10.62
MA0131.10.387
MA0135.10.471
MA0136.10.0888
MA0137.20.529
MA0138.20.649
MA0139.10.663
MA0140.10.103
MA0141.10.483
MA0142.10.663
MA0143.10.821
MA0144.10.844
MA0145.10.326
MA0146.10.268
MA0147.10.647
MA0148.10.353
MA0149.10.071
MA0150.10.336
MA0152.10.883
MA0153.10.533
MA0154.16.30876e-4
MA0155.10.696
MA0156.10.0242
MA0157.10.395
MA0159.10.0143
MA0160.10.451
MA0162.10.322
MA0163.18.29119e-6
MA0164.10.822
MA0258.12.11774e-4
MA0259.10.71



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: CNhs12010

Novel motifP-value
10.216
100.139
1000.85
1010.216
1020.706
1030.433
1040.732
1050.59
1060.00474
1070.35
1080.666
1090.246
110.144
1100.947
1110.478
1120.13
1130.154
1140.146
1150.871
1160.286
1170.581
1180.45
1190.242
120.918
1200.58
1210.132
1220.748
1230.0207
1240.0193
1250.31
1260.414
1270.385
1280.0588
1290.983
130.528
1300.193
1310.0631
1320.794
1330.965
1340.898
1350.885
1360.0612
1370.108
1380.914
1396.24976e-4
140.37
1400.172
1410.6
1420.08
1430.103
1440.505
1450.368
1460.906
1470.63
1480.0119
1490.525
150.192
1500.672
1510.283
1520.895
1530.0257
1540.544
1550.212
1560.154
1570.0394
1580.18
1590.335
160.112
1600.746
1610.128
1620.645
1630.882
1640.922
1650.411
1660.506
1670.0699
1680.668
1690.121
170.186
180.0279
190.268
20.608
200.578
210.4
220.511
230.0939
240.535
250.453
260.087
270.245
280.406
290.24
30.0598
300.697
310.337
327.60701e-4
330.737
340.601
350.0468
360.89
370.114
380.643
390.909
40.488
400.598
410.96
420.582
430.09
440.175
450.614
460.0267
470.353
480.594
490.104
50.188
500.933
510.502
520.317
530.509
540.34
550.135
560.432
570.527
580.0552
590.171
60.147
600.0445
610.578
620.0396
630.367
640.173
650.176
660.123
670.652
680.872
690.552
70.507
701.46095e-4
710.0321
720.85
730.989
740.953
750.434
760.821
770.0529
780.857
790.0306
80.515
800.407
810.0775
820.043
830.894
840.977
850.0145
860.519
870.504
880.309
890.0333
90.709
900.564
910.888
920.0989
930.741
940.0209
950.688
960.351
970.442
980.255
990.352



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: CNhs12010


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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