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FF:11317-117D3: 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, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelymph node
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 number2714
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-0.106
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-0.0905
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11901

Jaspar motifP-value
MA0002.20.00749
MA0003.10.203
MA0004.10.121
MA0006.10.483
MA0007.10.85
MA0009.10.123
MA0014.10.969
MA0017.10.109
MA0018.28.3477e-4
MA0019.10.147
MA0024.10.148
MA0025.10.108
MA0027.10.92
MA0028.10.945
MA0029.10.677
MA0030.10.105
MA0031.10.079
MA0035.20.406
MA0038.10.933
MA0039.20.609
MA0040.10.359
MA0041.10.0302
MA0042.10.0676
MA0043.19.95606e-5
MA0046.10.392
MA0047.20.0137
MA0048.10.392
MA0050.10.0183
MA0051.17.23659e-4
MA0052.10.86
MA0055.10.465
MA0057.10.462
MA0058.10.00929
MA0059.10.448
MA0060.10.944
MA0061.10.0285
MA0062.20.824
MA0065.20.00241
MA0066.10.216
MA0067.10.479
MA0068.10.515
MA0069.10.107
MA0070.10.295
MA0071.10.133
MA0072.10.637
MA0073.10.311
MA0074.10.917
MA0076.10.58
MA0077.16.20162e-6
MA0078.10.123
MA0079.20.366
MA0080.27.64063e-4
MA0081.10.109
MA0083.10.344
MA0084.10.0187
MA0087.10.0531
MA0088.10.924
MA0090.10.183
MA0091.10.389
MA0092.10.13
MA0093.10.0774
MA0099.20.0141
MA0100.10.786
MA0101.10.382
MA0102.20.0504
MA0103.10.00534
MA0104.20.281
MA0105.10.00348
MA0106.10.00515
MA0107.10.507
MA0108.20.00349
MA0111.10.78
MA0112.20.00145
MA0113.10.854
MA0114.10.0219
MA0115.10.0336
MA0116.12.06051e-5
MA0117.10.12
MA0119.10.16
MA0122.10.368
MA0124.10.538
MA0125.10.695
MA0131.10.162
MA0135.10.169
MA0136.10.0546
MA0137.20.332
MA0138.20.202
MA0139.10.746
MA0140.10.101
MA0141.10.398
MA0142.10.0935
MA0143.10.422
MA0144.10.414
MA0145.10.891
MA0146.10.0533
MA0147.10.19
MA0148.10.00385
MA0149.10.231
MA0150.10.549
MA0152.10.872
MA0153.10.859
MA0154.10.00438
MA0155.10.944
MA0156.10.00371
MA0157.10.228
MA0159.10.874
MA0160.10.439
MA0162.10.668
MA0163.17.38857e-4
MA0164.10.396
MA0258.10.0622
MA0259.10.573



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: CNhs11901

Novel motifP-value
10.246
100.12
1000.787
1010.664
1020.556
1030.349
1040.407
1050.248
1060.0166
1070.559
1080.808
1090.171
110.263
1100.66
1110.827
1120.335
1130.4
1140.558
1150.0526
1160.00774
1170.723
1180.628
1190.447
120.485
1200.939
1210.748
1220.848
1230.445
1240.111
1250.953
1260.346
1270.0593
1280.227
1290.633
130.719
1300.595
1310.593
1320.279
1330.565
1340.625
1350.154
1360.293
1370.432
1380.162
1390.607
140.691
1400.0876
1410.719
1420.0152
1430.515
1440.202
1450.536
1460.91
1470.461
1480.218
1490.362
150.42
1500.82
1510.518
1520.371
1530.146
1540.556
1550.159
1560.0798
1570.33
1580.316
1590.157
160.148
1600.774
1610.0378
1620.262
1630.771
1640.813
1650.939
1660.677
1670.289
1680.902
1690.791
170.384
180.0257
190.221
20.349
200.229
210.906
220.499
230.703
240.348
250.213
260.0351
270.473
280.5
290.339
30.475
300.421
310.257
320.027
330.744
340.902
350.321
360.199
370.715
380.848
390.0952
40.0204
400.695
410.437
420.712
430.098
440.074
450.739
460.116
470.25
480.52
490.08
50.885
500.813
510.564
520.296
530.464
540.615
550.911
560.489
570.966
580.0411
590.145
60.294
600.0605
610.761
620.0102
630.278
640.0422
650.292
660.752
670.595
680.939
690.356
70.474
700.0327
710.117
720.546
730.251
740.487
750.707
760.861
770.164
780.571
790.631
80.315
800.434
810.226
820.291
830.512
840.745
850.0723
860.948
870.819
880.179
890.241
90.338
900.269
910.397
920.144
930.193
940.233
950.8
960.799
970.264
980.509
990.881



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: CNhs11901


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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