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FF:11342-117G1: 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 16:47, 29 March 2012


Name:Endothelial Cells - Microvascular, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecapillary
dev stage47 years old adult
sexfemale
age47
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 number1941
catalog numberCA100-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-0.169
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-lymphoma-0.0876
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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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: CNhs11376

Jaspar motifP-value
MA0002.20.794
MA0003.10.325
MA0004.10.578
MA0006.10.108
MA0007.10.0992
MA0009.10.607
MA0014.10.293
MA0017.10.11
MA0018.20.00942
MA0019.10.194
MA0024.10.0166
MA0025.10.376
MA0027.10.968
MA0028.10.634
MA0029.10.929
MA0030.10.791
MA0031.10.571
MA0035.20.00646
MA0038.10.194
MA0039.20.183
MA0040.10.116
MA0041.10.199
MA0042.10.558
MA0043.14.74083e-6
MA0046.10.352
MA0047.20.207
MA0048.10.487
MA0050.10.0253
MA0051.10.912
MA0052.10.867
MA0055.10.0626
MA0057.10.736
MA0058.10.441
MA0059.10.164
MA0060.10.464
MA0061.10.237
MA0062.20.755
MA0065.20.0297
MA0066.10.342
MA0067.10.141
MA0068.10.844
MA0069.10.464
MA0070.10.184
MA0071.10.292
MA0072.10.194
MA0073.10.323
MA0074.10.857
MA0076.10.106
MA0077.17.82093e-5
MA0078.10.00333
MA0079.20.792
MA0080.20.00333
MA0081.10.11
MA0083.10.249
MA0084.10.257
MA0087.10.0572
MA0088.10.18
MA0090.10.653
MA0091.10.971
MA0092.10.145
MA0093.10.661
MA0099.21.81634e-8
MA0100.10.135
MA0101.10.0212
MA0102.23.16344e-4
MA0103.10.591
MA0104.20.96
MA0105.10.0977
MA0106.10.0123
MA0107.10.0126
MA0108.20.107
MA0111.10.974
MA0112.20.0323
MA0113.10.807
MA0114.10.172
MA0115.10.999
MA0116.10.184
MA0117.10.103
MA0119.10.008
MA0122.10.0676
MA0124.10.519
MA0125.10.793
MA0131.10.373
MA0135.10.545
MA0136.10.00381
MA0137.20.305
MA0138.20.134
MA0139.10.251
MA0140.10.00379
MA0141.10.0907
MA0142.10.875
MA0143.10.985
MA0144.10.381
MA0145.10.0574
MA0146.10.335
MA0147.10.766
MA0148.10.0513
MA0149.10.0583
MA0150.10.0181
MA0152.10.843
MA0153.10.483
MA0154.10.12
MA0155.10.115
MA0156.10.0066
MA0157.10.67
MA0159.10.08
MA0160.10.276
MA0162.10.0877
MA0163.10.139
MA0164.10.606
MA0258.10.165
MA0259.10.876



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: CNhs11376

Novel motifP-value
10.0277
100.987
1000.274
1010.152
1020.752
1030.682
1040.768
1050.672
1060.143
1070.0647
1080.528
1090.0798
110.0423
1100.0531
1110.152
1120.45
1130.664
1140.0959
1150.363
1160.529
1170.436
1180.491
1190.111
120.781
1200.0519
1210.336
1220.215
1230.484
1240.236
1250.173
1260.287
1270.52
1280.448
1290.186
130.148
1300.911
1310.988
1320.437
1330.229
1340.863
1350.00758
1360.294
1370.521
1380.674
1390.257
140.673
1400.548
1410.354
1420.685
1430.133
1440.691
1450.115
1460.0728
1470.0894
1480.852
1490.0671
150.239
1500.256
1510.374
1520.0318
1530.684
1540.15
1550.871
1560.181
1570.288
1580.578
1590.234
160.272
1600.0893
1610.475
1620.948
1630.624
1640.117
1650.908
1660.362
1670.285
1680.852
1690.0209
170.2
180.145
190.168
20.809
200.878
210.8
220.128
230.315
240.367
250.833
260.328
270.119
280.251
290.373
30.343
300.774
310.648
320.885
330.0517
340.449
350.813
360.00265
370.0765
380.0952
390.836
40.877
400.00217
410.105
420.565
430.373
440.273
450.327
460.049
470.111
480.0552
490.433
50.259
500.721
510.245
520.673
530.885
540.569
550.594
560.621
570.111
580.788
590.0728
60.423
600.94
610.995
620.94
630.298
640.186
650.144
660.423
670.325
680.455
690.671
70.234
700.0467
710.201
720.923
730.00428
740.966
750.152
760.673
770.297
780.228
790.569
80.00739
800.705
810.981
820.322
830.841
840.115
850.206
860.926
870.0537
880.976
890.174
90.494
900.545
910.827
920.226
930.994
940.796
950.0822
960.254
970.382
980.0579
990.0152



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: CNhs11376


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)
0002144 (capillary endothelial cell)
0002321 (embryonic cell)
0002371 (somatic 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)
0001915 (endothelium of capillary)
0001981 (blood vessel)
0001982 (capillary)
0001986 (endothelium)
0002049 (vasculature)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004535 (cardiovascular system)
0004537 (blood vasculature)
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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