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FF:12382-131E6: 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 17:29, 29 March 2012


Name:Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep2 (MM XIV - 1)
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 stageNA
sexNA
ageNA
cell typeendothelial cell, lymphatic
cell lineNA
companyNA
collaborationMichael Detmar (Swiss Federal Institute of Technology, ETH Zurich)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
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-penis0.305
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-lymphoma0.0339
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
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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: CNhs13157

Jaspar motifP-value
MA0002.20.55
MA0003.10.457
MA0004.10.334
MA0006.10.176
MA0007.10.0698
MA0009.10.758
MA0014.10.996
MA0017.10.115
MA0018.20.0119
MA0019.10.636
MA0024.10.309
MA0025.10.0976
MA0027.10.805
MA0028.10.278
MA0029.10.539
MA0030.10.01
MA0031.10.0712
MA0035.20.233
MA0038.10.1
MA0039.20.635
MA0040.10.252
MA0041.10.865
MA0042.10.359
MA0043.15.73775e-4
MA0046.10.331
MA0047.20.943
MA0048.10.0884
MA0050.10.0115
MA0051.13.89339e-4
MA0052.10.0861
MA0055.10.0379
MA0057.10.976
MA0058.10.157
MA0059.10.0385
MA0060.10.0554
MA0061.10.00131
MA0062.20.024
MA0065.20.0158
MA0066.10.0657
MA0067.10.207
MA0068.10.963
MA0069.10.569
MA0070.10.042
MA0071.10.419
MA0072.10.545
MA0073.10.554
MA0074.10.264
MA0076.10.00297
MA0077.11.42201e-5
MA0078.10.0133
MA0079.20.17
MA0080.20.898
MA0081.10.875
MA0083.10.522
MA0084.10.375
MA0087.10.309
MA0088.10.391
MA0090.10.417
MA0091.10.298
MA0092.10.0587
MA0093.10.351
MA0099.20.653
MA0100.10.223
MA0101.11.97057e-7
MA0102.20.813
MA0103.10.509
MA0104.20.618
MA0105.12.15799e-4
MA0106.10.00488
MA0107.11.83765e-6
MA0108.20.0168
MA0111.10.745
MA0112.20.00767
MA0113.10.235
MA0114.10.181
MA0115.10.879
MA0116.10.0122
MA0117.10.512
MA0119.10.00293
MA0122.10.527
MA0124.10.915
MA0125.10.537
MA0131.10.976
MA0135.10.154
MA0136.10.607
MA0137.20.884
MA0138.20.123
MA0139.10.335
MA0140.10.391
MA0141.10.141
MA0142.10.989
MA0143.10.962
MA0144.10.153
MA0145.10.364
MA0146.10.366
MA0147.10.389
MA0148.10.496
MA0149.10.0417
MA0150.10.736
MA0152.10.371
MA0153.10.144
MA0154.10.0453
MA0155.10.302
MA0156.10.894
MA0157.10.766
MA0159.10.0186
MA0160.10.846
MA0162.10.0341
MA0163.10.00317
MA0164.10.381
MA0258.10.0178
MA0259.10.863



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: CNhs13157

Novel motifP-value
10.0611
100.284
1000.0437
1010.51
1020.771
1030.576
1040.658
1050.81
1060.00616
1070.0243
1080.0493
1090.0655
110.0438
1100.0223
1110.055
1120.649
1130.781
1140.0749
1150.662
1160.406
1170.181
1180.577
1190.0176
120.874
1200.285
1210.697
1220.308
1230.047
1240.0325
1250.065
1260.914
1270.451
1280.208
1290.741
130.00599
1300.296
1310.706
1320.385
1330.461
1340.693
1350.196
1360.363
1370.498
1380.648
1390.186
140.617
1400.575
1410.224
1420.701
1430.0637
1440.537
1450.0355
1460.467
1470.141
1480.406
1490.357
150.418
1500.166
1510.567
1520.0455
1530.778
1540.58
1550.951
1560.231
1570.153
1580.4
1590.183
160.244
1600.00508
1610.913
1620.429
1630.904
1640.176
1650.577
1660.882
1670.134
1680.293
1690.0178
170.0512
180.541
190.109
20.852
200.337
210.441
220.487
230.481
240.962
250.51
260.0899
270.626
280.584
290.293
30.167
300.191
310.549
320.227
330.0538
340.851
350.136
360.00408
370.0394
380.208
390.365
40.615
400.00425
410.207
420.474
430.282
440.982
450.69
460.0624
470.138
480.101
490.317
50.535
500.585
510.498
520.818
530.755
540.608
550.934
560.445
570.0859
580.901
590.214
60.919
600.401
610.811
620.764
630.0936
640.342
650.17
660.911
670.131
680.211
690.526
70.738
700.104
710.0683
720.585
730.00938
740.173
750.153
760.39
770.409
780.0419
790.0469
80.00292
800.448
810.699
820.361
830.922
840.562
850.158
860.658
870.111
880.652
890.145
90.959
900.191
910.408
920.153
930.589
940.661
950.0583
960.453
970.518
980.305
990.0812



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: CNhs13157


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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