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FF:11265-116G5: 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 17:01, 29 March 2012


Name:Endothelial Cells - Microvascular, donor1
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 stage53 years old adult
sexfemale
age53
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 number2522
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-0.118
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-0.0196
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
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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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: CNhs11925

Jaspar motifP-value
MA0002.20.456
MA0003.10.365
MA0004.10.92
MA0006.10.0224
MA0007.10.178
MA0009.10.691
MA0014.10.63
MA0017.10.316
MA0018.22.24083e-5
MA0019.10.0305
MA0024.10.027
MA0025.10.36
MA0027.10.734
MA0028.10.16
MA0029.10.516
MA0030.10.706
MA0031.10.294
MA0035.20.0356
MA0038.10.687
MA0039.20.22
MA0040.10.158
MA0041.10.185
MA0042.10.433
MA0043.11.51192e-6
MA0046.10.561
MA0047.20.128
MA0048.10.541
MA0050.10.522
MA0051.10.656
MA0052.10.574
MA0055.10.12
MA0057.10.534
MA0058.10.747
MA0059.10.958
MA0060.10.755
MA0061.10.146
MA0062.20.106
MA0065.20.0671
MA0066.10.384
MA0067.10.0564
MA0068.10.723
MA0069.10.0462
MA0070.10.87
MA0071.10.285
MA0072.10.475
MA0073.10.41
MA0074.10.705
MA0076.10.00768
MA0077.16.27218e-9
MA0078.10.00504
MA0079.20.419
MA0080.20.0317
MA0081.10.417
MA0083.10.834
MA0084.10.959
MA0087.10.152
MA0088.10.722
MA0090.10.0514
MA0091.10.106
MA0092.10.255
MA0093.10.942
MA0099.20.0021
MA0100.10.111
MA0101.16.64125e-4
MA0102.24.66557e-4
MA0103.10.622
MA0104.20.118
MA0105.10.534
MA0106.10.00257
MA0107.19.33274e-4
MA0108.20.431
MA0111.10.713
MA0112.20.185
MA0113.10.169
MA0114.10.483
MA0115.10.524
MA0116.10.589
MA0117.10.0323
MA0119.10.299
MA0122.10.408
MA0124.10.829
MA0125.10.81
MA0131.10.519
MA0135.10.988
MA0136.10.282
MA0137.20.142
MA0138.20.0853
MA0139.10.247
MA0140.10.192
MA0141.10.106
MA0142.10.269
MA0143.10.78
MA0144.10.407
MA0145.10.157
MA0146.10.141
MA0147.10.176
MA0148.10.0474
MA0149.10.117
MA0150.10.696
MA0152.10.942
MA0153.10.844
MA0154.10.178
MA0155.10.0464
MA0156.10.0598
MA0157.10.196
MA0159.10.0944
MA0160.10.993
MA0162.10.0583
MA0163.10.649
MA0164.10.8
MA0258.10.305
MA0259.10.124



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: CNhs11925

Novel motifP-value
10.467
100.601
1000.194
1010.327
1020.557
1030.586
1040.977
1050.659
1060.0514
1070.0325
1080.798
1090.0264
110.0929
1100.129
1110.238
1120.425
1130.383
1140.245
1150.934
1160.273
1170.377
1180.778
1190.283
120.858
1200.0327
1210.719
1220.846
1230.165
1240.157
1250.884
1260.814
1270.383
1280.514
1290.152
130.125
1300.566
1310.333
1320.0692
1330.179
1340.743
1350.0763
1360.16
1370.435
1380.911
1390.66
140.885
1400.0888
1410.672
1420.567
1430.153
1440.667
1450.194
1460.338
1470.136
1480.463
1490.00857
150.807
1500.223
1510.523
1520.0385
1530.412
1540.0931
1550.797
1560.935
1570.891
1580.22
1590.434
160.384
1600.1
1610.947
1620.929
1630.865
1640.373
1650.455
1660.258
1670.0466
1680.206
1690.0276
170.11
180.884
190.172
20.375
200.819
210.993
220.126
230.201
240.48
250.53
260.887
270.123
280.216
290.445
30.613
300.841
310.52
320.432
330.0576
340.144
350.779
360.0254
370.165
380.076
390.175
40.772
401.17394e-4
410.074
420.93
430.483
440.288
450.258
460.296
470.939
480.209
490.752
50.846
500.248
510.485
520.86
530.74
540.468
550.6
560.52
570.747
580.368
590.109
60.046
600.634
610.629
620.603
630.437
640.636
650.0845
660.368
670.645
680.115
690.736
70.767
700.612
710.863
720.934
730.00862
740.178
750.321
760.449
770.054
780.31
790.067
80.0378
800.791
810.538
820.444
830.384
840.194
850.533
860.933
870.0597
880.97
890.167
90.471
900.264
910.865
920.338
930.303
940.669
950.0648
960.632
970.227
980.356
990.0467



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: CNhs11925


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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