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FF:11414-118F1: 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 17:07, 29 March 2012


Name:Endothelial Cells - Microvascular, donor3
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 number2548
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-penis0.169
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-0.152
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: CNhs12024

Jaspar motifP-value
MA0002.20.117
MA0003.10.551
MA0004.10.891
MA0006.10.0313
MA0007.10.254
MA0009.10.901
MA0014.10.886
MA0017.10.941
MA0018.21.44507e-4
MA0019.10.0778
MA0024.10.155
MA0025.10.285
MA0027.10.925
MA0028.10.00382
MA0029.10.643
MA0030.10.878
MA0031.10.93
MA0035.20.158
MA0038.10.104
MA0039.20.336
MA0040.10.583
MA0041.10.161
MA0042.10.758
MA0043.11.26264e-5
MA0046.10.901
MA0047.20.681
MA0048.10.336
MA0050.10.649
MA0051.10.837
MA0052.10.649
MA0055.10.129
MA0057.10.576
MA0058.10.906
MA0059.10.458
MA0060.10.271
MA0061.10.973
MA0062.22.80267e-5
MA0065.20.295
MA0066.10.79
MA0067.10.0614
MA0068.10.675
MA0069.10.0587
MA0070.10.961
MA0071.10.898
MA0072.10.9
MA0073.10.822
MA0074.10.255
MA0076.11.27196e-5
MA0077.19.35597e-11
MA0078.10.0106
MA0079.20.236
MA0080.20.371
MA0081.10.671
MA0083.10.679
MA0084.10.699
MA0087.10.299
MA0088.10.394
MA0090.10.154
MA0091.10.114
MA0092.10.652
MA0093.10.975
MA0099.20.00785
MA0100.10.0402
MA0101.10.0305
MA0102.22.16765e-5
MA0103.10.264
MA0104.20.0338
MA0105.10.321
MA0106.10.0338
MA0107.10.0235
MA0108.20.256
MA0111.10.396
MA0112.20.803
MA0113.10.624
MA0114.10.911
MA0115.10.474
MA0116.10.185
MA0117.10.0213
MA0119.10.511
MA0122.10.565
MA0124.10.863
MA0125.10.787
MA0131.10.76
MA0135.10.289
MA0136.10.0337
MA0137.20.0201
MA0138.20.116
MA0139.10.923
MA0140.10.891
MA0141.10.457
MA0142.10.457
MA0143.10.94
MA0144.10.942
MA0145.10.411
MA0146.10.145
MA0147.10.033
MA0148.10.329
MA0149.10.184
MA0150.10.0344
MA0152.10.386
MA0153.10.383
MA0154.10.933
MA0155.10.0764
MA0156.10.259
MA0157.10.697
MA0159.10.996
MA0160.10.477
MA0162.10.334
MA0163.10.109
MA0164.10.265
MA0258.10.502
MA0259.10.036



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: CNhs12024

Novel motifP-value
10.422
100.0721
1000.222
1010.0846
1020.611
1030.96
1040.876
1050.296
1060.0578
1070.00983
1080.349
1090.39
110.507
1100.306
1110.672
1120.709
1130.202
1140.995
1150.281
1160.556
1170.854
1180.908
1190.286
120.849
1200.0713
1210.998
1220.905
1230.163
1240.00486
1250.615
1260.711
1270.223
1280.865
1290.343
130.587
1300.403
1310.0415
1320.017
1330.0235
1340.917
1350.903
1360.014
1370.102
1380.837
1390.713
140.672
1400.105
1411
1420.746
1430.637
1440.825
1450.276
1460.517
1470.0837
1480.249
1490.143
150.236
1500.0632
1510.754
1520.00642
1530.536
1540.0798
1550.793
1560.428
1571
1580.147
1590.859
160.675
1600.14
1610.741
1620.743
1630.7
1640.302
1650.112
1660.588
1670.178
1680.709
1690.0949
170.322
180.272
190.204
20.822
200.672
210.83
220.268
230.932
240.951
250.131
260.674
270.299
280.157
290.437
30.737
300.992
310.378
320.179
330.317
340.404
350.184
360.152
370.535
380.336
390.421
40.83
400.00532
410.822
420.433
430.587
440.779
450.364
460.982
470.971
480.757
490.34
50.537
500.512
510.895
520.776
530.218
540.778
550.298
560.665
570.864
580.0736
590.166
60.0643
600.877
610.202
620.119
630.667
640.85
650.27
660.744
670.951
680.0708
690.636
70.224
700.64
710.0683
720.37
730.00172
740.411
750.686
760.441
770.279
780.747
790.0191
80.0983
800.0615
810.402
820.667
830.274
840.191
850.638
860.82
870.0822
880.994
890.462
90.854
900.18
910.74
920.764
930.856
940.244
950.0571
960.446
970.354
980.811
990.0286



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: CNhs12024


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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