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FF:11393-118C7: 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 17:00, 29 March 2012


Name:Endothelial Cells - Lymphatic, 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 stagefetus
sexunknown
agefetal
cell typeendothelial cell, lymphatic
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3676
catalog numberSC2015
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-0.155
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-lymphoma0.021
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
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: CNhs11906

Jaspar motifP-value
MA0002.20.00264
MA0003.10.305
MA0004.10.797
MA0006.10.451
MA0007.10.619
MA0009.10.641
MA0014.10.922
MA0017.10.036
MA0018.20.0222
MA0019.10.0303
MA0024.10.776
MA0025.10.468
MA0027.10.675
MA0028.10.864
MA0029.10.819
MA0030.10.144
MA0031.10.0241
MA0035.20.315
MA0038.10.269
MA0039.20.688
MA0040.10.274
MA0041.10.0814
MA0042.10.176
MA0043.10.0143
MA0046.10.938
MA0047.20.00525
MA0048.10.871
MA0050.10.808
MA0051.10.135
MA0052.10.785
MA0055.10.865
MA0057.10.191
MA0058.10.405
MA0059.10.22
MA0060.10.234
MA0061.10.174
MA0062.20.817
MA0065.20.00188
MA0066.10.0648
MA0067.10.806
MA0068.10.319
MA0069.10.0427
MA0070.10.921
MA0071.10.384
MA0072.10.403
MA0073.10.811
MA0074.10.765
MA0076.10.73
MA0077.14.68116e-8
MA0078.10.012
MA0079.20.671
MA0080.22.16792e-4
MA0081.10.0805
MA0083.10.857
MA0084.10.1
MA0087.10.0359
MA0088.10.637
MA0090.10.104
MA0091.10.453
MA0092.10.596
MA0093.10.697
MA0099.20.527
MA0100.10.677
MA0101.10.0626
MA0102.20.0194
MA0103.10.00734
MA0104.20.162
MA0105.10.0103
MA0106.10.109
MA0107.10.116
MA0108.20.0794
MA0111.10.649
MA0112.24.84369e-4
MA0113.10.853
MA0114.10.0182
MA0115.10.00994
MA0116.19.2125e-5
MA0117.10.37
MA0119.10.799
MA0122.10.266
MA0124.10.435
MA0125.10.974
MA0131.10.0924
MA0135.10.351
MA0136.10.0179
MA0137.20.7
MA0138.20.296
MA0139.10.854
MA0140.10.124
MA0141.10.128
MA0142.10.363
MA0143.10.593
MA0144.10.525
MA0145.10.953
MA0146.10.0333
MA0147.10.135
MA0148.10.00198
MA0149.10.74
MA0150.10.576
MA0152.10.992
MA0153.10.797
MA0154.10.0092
MA0155.10.614
MA0156.13.07113e-4
MA0157.10.0956
MA0159.10.658
MA0160.10.0962
MA0162.10.511
MA0163.11.62069e-4
MA0164.10.221
MA0258.10.019
MA0259.10.395



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: CNhs11906

Novel motifP-value
10.232
100.0673
1000.728
1010.389
1020.422
1030.807
1040.765
1050.0873
1060.11
1070.412
1080.61
1090.0777
110.0894
1100.88
1110.677
1120.288
1130.856
1140.491
1150.118
1160.00262
1170.628
1180.324
1190.428
120.506
1200.15
1210.44
1220.401
1230.108
1240.0265
1250.503
1260.571
1270.0939
1280.0974
1290.875
130.585
1300.863
1310.303
1320.675
1330.999
1340.985
1350.215
1360.455
1370.656
1380.82
1390.296
140.514
1400.0342
1410.739
1420.0176
1430.324
1440.0908
1450.725
1460.837
1470.26
1480.0108
1490.324
150.214
1500.893
1510.401
1520.458
1530.387
1540.588
1550.22
1560.058
1570.376
1580.978
1590.786
160.0793
1600.298
1610.0134
1620.438
1630.358
1640.494
1650.845
1660.356
1670.104
1680.753
1690.286
170.451
180.0173
190.565
20.453
200.471
210.357
220.296
230.924
240.765
250.217
260.00897
270.368
280.905
290.392
30.207
300.632
310.48
320.0226
330.913
340.877
350.381
360.144
370.46
380.994
390.256
40.211
400.629
410.236
420.488
430.0865
440.0211
450.966
460.0648
470.062
480.259
490.11
50.653
500.658
510.365
520.251
530.59
540.335
550.819
560.232
570.571
580.0891
590.0864
60.108
600.0711
610.328
620.0325
630.229
640.0277
650.292
660.579
670.336
680.956
690.294
70.213
700.00288
710.091
720.895
730.622
740.539
750.552
760.864
770.0239
780.383
790.632
80.0861
800.717
810.184
820.327
830.851
840.206
850.118
860.887
870.328
880.228
890.237
90.431
900.339
910.596
920.541
930.845
940.125
950.474
960.413
970.392
980.0577
990.768



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: CNhs11906


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)
0000115 (endothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002138 (endothelial cell of lymphatic vessel)
0002139 (endothelial cell of vascular tree)
0002321 (embryonic cell)
0002371 (somatic cell)

UBERON: Anatomy
0000055 (vessel)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000480 (anatomical group)
0001009 (circulatory system)
0001062 (anatomical entity)
0001473 (lymphatic vessel)
0002049 (vasculature)
0002193 (hemolymphoid system)
0002405 (immune system)
0002465 (lymphoid system)
0004111 (anatomical conduit)
0004535 (cardiovascular system)
0004536 (lymph vasculature)
0006558 (lymphatic part of lymphoid system)
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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