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FF:11236-116D3: 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 16:35, 29 March 2012


Name:Endothelial Cells - Lymphatic, donor1
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 number3719
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-0.0854
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-0.116
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: CNhs10865

Jaspar motifP-value
MA0002.21.66459e-4
MA0003.10.292
MA0004.10.0518
MA0006.10.218
MA0007.10.565
MA0009.10.227
MA0014.10.532
MA0017.10.15
MA0018.25.21013e-6
MA0019.10.856
MA0024.10.0857
MA0025.10.00898
MA0027.10.46
MA0028.10.962
MA0029.10.799
MA0030.10.754
MA0031.10.523
MA0035.20.627
MA0038.10.3
MA0039.20.955
MA0040.10.917
MA0041.10.934
MA0042.10.762
MA0043.15.26654e-6
MA0046.10.461
MA0047.20.123
MA0048.10.0271
MA0050.10.323
MA0051.10.0672
MA0052.10.183
MA0055.10.0231
MA0057.10.695
MA0058.10.0027
MA0059.10.928
MA0060.10.131
MA0061.10.016
MA0062.20.159
MA0065.20.194
MA0066.10.352
MA0067.10.937
MA0068.10.143
MA0069.10.0115
MA0070.10.235
MA0071.10.476
MA0072.10.334
MA0073.10.372
MA0074.10.737
MA0076.10.0525
MA0077.16.70123e-6
MA0078.10.0608
MA0079.20.806
MA0080.20.0599
MA0081.10.214
MA0083.10.0882
MA0084.10.091
MA0087.10.0962
MA0088.10.308
MA0090.10.162
MA0091.10.201
MA0092.10.65
MA0093.10.0384
MA0099.20.162
MA0100.10.504
MA0101.10.683
MA0102.20.00237
MA0103.10.0217
MA0104.20.297
MA0105.10.0617
MA0106.18.81929e-4
MA0107.10.564
MA0108.24.43548e-7
MA0111.10.391
MA0112.20.0162
MA0113.10.852
MA0114.10.153
MA0115.10.364
MA0116.18.33577e-4
MA0117.10.168
MA0119.10.0189
MA0122.10.401
MA0124.10.392
MA0125.10.549
MA0131.10.103
MA0135.10.141
MA0136.10.183
MA0137.20.15
MA0138.20.436
MA0139.10.376
MA0140.10.197
MA0141.10.686
MA0142.10.0991
MA0143.10.591
MA0144.10.952
MA0145.10.874
MA0146.10.23
MA0147.10.264
MA0148.10.0945
MA0149.10.0483
MA0150.10.715
MA0152.10.464
MA0153.10.291
MA0154.10.0313
MA0155.10.82
MA0156.10.0979
MA0157.10.397
MA0159.10.431
MA0160.10.801
MA0162.10.51
MA0163.10.193
MA0164.10.528
MA0258.10.155
MA0259.10.523



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: CNhs10865

Novel motifP-value
10.35
100.919
1000.217
1010.945
1020.622
1030.554
1040.518
1050.19
1060.18
1070.729
1080.755
1090.762
110.797
1100.215
1110.357
1120.866
1130.959
1140.52
1150.134
1160.463
1170.598
1180.531
1190.335
120.46
1200.156
1210.568
1220.452
1230.334
1240.0458
1250.846
1260.824
1270.077
1280.667
1290.276
130.353
1300.388
1310.567
1320.25
1330.905
1340.42
1350.539
1360.128
1370.293
1380.279
1390.323
140.892
1400.353
1410.644
1423.63791e-4
1430.68
1440.852
1450.019
1460.445
1470.53
1480.0791
1490.526
150.602
1500.62
1510.985
1520.207
1530.491
1540.937
1550.401
1560.211
1570.768
1580.238
1590.118
160.396
1600.55
1610.0328
1620.537
1630.846
1640.201
1650.695
1660.37
1670.734
1680.921
1690.569
170.68
180.0662
190.354
20.173
200.021
210.267
220.79
230.609
240.555
250.11
260.437
270.196
280.535
290.816
30.469
300.0422
310.409
320.146
330.618
340.746
350.274
360.0722
370.229
380.458
390.059
40.0201
400.313
410.272
420.594
430.3
440.672
450.929
460.652
470.984
480.411
490.466
50.798
500.72
510.784
520.272
530.992
540.843
550.363
560.692
570.22
580.0109
590.248
60.564
600.0596
610.913
620.0254
630.751
640.262
650.607
660.85
670.668
680.332
690.674
70.413
700.299
710.366
720.961
730.0195
740.786
750.382
760.251
770.42
780.35
790.642
80.218
800.209
810.412
820.901
830.932
840.636
850.593
860.937
870.956
880.239
890.25
90.12
900.0805
910.495
920.121
930.168
940.362
950.358
960.693
970.347
980.498
990.22



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: CNhs10865


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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