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FF:11324-117E1: 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 17:03, 29 March 2012


Name:Endothelial Cells - Umbilical vein, donor2
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 number2205
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-0.0126
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-lymphoma0.409
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: CNhs11967

Jaspar motifP-value
MA0002.23.71519e-5
MA0003.10.684
MA0004.10.917
MA0006.10.676
MA0007.10.73
MA0009.10.51
MA0014.10.836
MA0017.10.131
MA0018.20.0386
MA0019.10.1
MA0024.14.23748e-5
MA0025.10.0495
MA0027.10.622
MA0028.10.824
MA0029.10.392
MA0030.10.714
MA0031.10.652
MA0035.20.0151
MA0038.10.0116
MA0039.20.716
MA0040.10.396
MA0041.10.00696
MA0042.10.218
MA0043.17.50241e-5
MA0046.10.485
MA0047.20.878
MA0048.10.239
MA0050.10.627
MA0051.10.164
MA0052.10.286
MA0055.10.11
MA0057.10.907
MA0058.10.845
MA0059.10.262
MA0060.11.12488e-9
MA0061.17.19134e-4
MA0062.20.467
MA0065.20.0185
MA0066.10.126
MA0067.10.432
MA0068.10.227
MA0069.10.0344
MA0070.10.635
MA0071.10.996
MA0072.10.655
MA0073.10.87
MA0074.10.96
MA0076.10.296
MA0077.11.05316e-4
MA0078.10.0649
MA0079.20.229
MA0080.20.15
MA0081.10.395
MA0083.10.00449
MA0084.10.0152
MA0087.10.0463
MA0088.10.667
MA0090.10.977
MA0091.10.304
MA0092.10.26
MA0093.10.819
MA0099.20.417
MA0100.10.494
MA0101.10.337
MA0102.20.00143
MA0103.10.00205
MA0104.20.264
MA0105.18.61001e-6
MA0106.10.405
MA0107.10.117
MA0108.20.0994
MA0111.10.79
MA0112.28.03706e-7
MA0113.10.383
MA0114.10.0408
MA0115.10.398
MA0116.17.27104e-4
MA0117.10.386
MA0119.10.58
MA0122.10.306
MA0124.10.274
MA0125.10.843
MA0131.10.526
MA0135.10.979
MA0136.10.493
MA0137.20.949
MA0138.20.548
MA0139.10.634
MA0140.10.207
MA0141.10.485
MA0142.10.684
MA0143.10.346
MA0144.10.869
MA0145.10.181
MA0146.10.25
MA0147.10.314
MA0148.10.582
MA0149.10.0539
MA0150.10.116
MA0152.10.997
MA0153.10.419
MA0154.19.81761e-4
MA0155.10.973
MA0156.10.0911
MA0157.10.329
MA0159.10.0156
MA0160.10.36
MA0162.10.382
MA0163.18.45595e-5
MA0164.10.996
MA0258.12.23928e-4
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: CNhs11967

Novel motifP-value
10.226
100.171
1000.767
1010.348
1020.771
1030.364
1040.683
1050.587
1060.00656
1070.355
1080.631
1090.106
110.244
1100.879
1110.202
1120.153
1130.0963
1140.115
1150.626
1160.292
1170.563
1180.431
1190.325
120.923
1200.594
1210.421
1220.719
1230.22
1240.0216
1250.238
1260.524
1270.3
1280.299
1290.816
130.435
1300.159
1310.164
1320.929
1330.88
1340.601
1350.624
1360.0958
1370.0729
1380.947
1390.00718
140.465
1400.194
1410.697
1420.0252
1430.0389
1440.716
1450.578
1460.522
1470.926
1480.00168
1490.975
150.175
1500.693
1510.268
1520.868
1530.0106
1540.846
1550.172
1560.229
1570.0605
1580.134
1590.18
160.132
1600.997
1610.0574
1620.621
1630.758
1640.897
1650.33
1660.87
1670.0469
1680.429
1690.16
170.18
180.0171
190.299
20.521
200.418
210.502
220.451
230.0931
240.513
250.355
260.0605
270.254
280.54
290.189
30.141
300.687
310.305
320.00738
330.917
340.424
350.0713
360.792
370.183
380.874
390.898
40.29
400.381
410.901
420.74
430.066
440.119
450.766
460.0443
470.34
480.674
490.0885
50.0864
500.957
510.435
520.302
530.58
540.314
550.434
560.476
570.592
580.0739
590.213
60.153
600.0516
610.654
620.0468
630.31
640.293
650.214
660.238
670.608
680.899
690.775
70.663
705.18598e-4
710.0322
720.64
730.982
740.392
750.366
760.907
770.0547
780.649
790.0733
80.616
800.364
810.0818
820.0489
830.631
840.968
850.0267
860.754
870.653
880.272
890.0415
90.668
900.803
910.672
920.145
930.612
940.00809
950.457
960.411
970.385
980.391
990.392



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: CNhs11967


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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