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FF:12260-130A1: 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 17:02, 29 March 2012


Name:Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep1 (MM XIX - 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-penis0.11
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-lymphoma0.0269
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: CNhs11936

Jaspar motifP-value
MA0002.20.252
MA0003.10.326
MA0004.10.173
MA0006.10.0282
MA0007.10.111
MA0009.10.829
MA0014.10.617
MA0017.10.0838
MA0018.20.0326
MA0019.10.0547
MA0024.10.694
MA0025.10.827
MA0027.10.433
MA0028.10.922
MA0029.10.937
MA0030.10.804
MA0031.10.913
MA0035.20.0993
MA0038.10.807
MA0039.20.383
MA0040.10.0708
MA0041.10.382
MA0042.10.597
MA0043.10.0214
MA0046.10.55
MA0047.20.179
MA0048.10.284
MA0050.11.15482e-5
MA0051.15.01516e-7
MA0052.10.216
MA0055.10.0829
MA0057.10.993
MA0058.10.0387
MA0059.10.118
MA0060.10.741
MA0061.15.41752e-5
MA0062.20.762
MA0065.20.0571
MA0066.10.0677
MA0067.10.2
MA0068.10.872
MA0069.10.0818
MA0070.10.392
MA0071.10.917
MA0072.10.655
MA0073.10.582
MA0074.10.582
MA0076.10.0735
MA0077.16.07139e-8
MA0078.10.0266
MA0079.20.95
MA0080.20.00232
MA0081.10.387
MA0083.10.577
MA0084.10.019
MA0087.10.00778
MA0088.10.314
MA0090.10.0482
MA0091.10.49
MA0092.10.133
MA0093.10.15
MA0099.20.0123
MA0100.10.103
MA0101.13.8681e-14
MA0102.20.233
MA0103.10.94
MA0104.20.925
MA0105.10.0127
MA0106.10.00649
MA0107.15.77236e-14
MA0108.20.00895
MA0111.10.736
MA0112.20.0532
MA0113.10.231
MA0114.10.236
MA0115.10.716
MA0116.10.216
MA0117.10.403
MA0119.10.0387
MA0122.10.196
MA0124.10.324
MA0125.10.71
MA0131.10.905
MA0135.10.235
MA0136.10.00839
MA0137.20.0325
MA0138.20.371
MA0139.10.262
MA0140.10.128
MA0141.10.346
MA0142.10.747
MA0143.10.563
MA0144.10.00131
MA0145.10.218
MA0146.10.42
MA0147.10.917
MA0148.10.0557
MA0149.10.0875
MA0150.10.47
MA0152.10.57
MA0153.10.388
MA0154.10.0579
MA0155.10.122
MA0156.12.70911e-4
MA0157.10.278
MA0159.10.11
MA0160.10.722
MA0162.10.07
MA0163.10.22
MA0164.10.476
MA0258.10.156
MA0259.10.335



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: CNhs11936

Novel motifP-value
10.145
100.999
1000.104
1010.251
1020.942
1030.221
1040.744
1050.767
1060.0229
1070.0506
1080.156
1090.0247
110.0386
1100.0288
1110.594
1120.531
1130.291
1140.442
1150.839
1160.387
1170.221
1180.851
1190.0276
120.997
1200.0487
1210.515
1220.768
1230.202
1240.0285
1250.488
1260.757
1270.399
1280.89
1290.331
130.0164
1300.447
1310.273
1320.221
1330.854
1340.653
1350.0808
1360.352
1370.371
1380.977
1390.916
140.895
1400.255
1410.133
1420.473
1430.0427
1440.995
1450.0898
1460.254
1470.0658
1480.462
1490.0275
150.818
1500.239
1510.517
1520.0157
1530.202
1540.0619
1550.247
1560.2
1570.0459
1580.111
1590.187
160.344
1600.0448
1610.894
1620.992
1630.737
1640.388
1650.572
1660.707
1670.447
1680.0671
1690.0342
170.0958
180.855
190.0702
20.564
200.875
210.735
220.267
230.265
240.531
250.334
260.543
270.205
280.22
290.303
30.726
300.678
310.546
320.352
330.0381
340.471
350.719
360.00668
370.0749
380.107
390.475
40.731
403.92975e-4
410.128
420.807
430.631
440.276
450.345
460.359
470.277
480.0852
490.874
50.406
500.333
510.536
520.979
530.823
540.66
550.761
560.484
570.614
580.382
590.122
60.176
600.741
610.691
620.69
630.22
640.734
650.0855
660.58
670.358
680.54
690.969
70.878
700.778
710.268
720.402
730.00226
740.434
750.192
760.614
770.274
780.0618
790.236
80.0235
800.933
810.59
820.335
830.534
840.518
850.451
860.789
870.0188
880.845
890.213
90.669
900.825
910.676
920.144
930.866
940.569
950.00835
960.705
970.44
980.789
990.0233



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: CNhs11936


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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