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FF:12504-133A2: 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 17:31, 29 March 2012


Name:Lymphatic Endothelial cells response to VEGFC, 00hr00min, biol_rep3 (MM XXII - 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-penis0.436
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-lymphoma0.0686
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
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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: CNhs13276

Jaspar motifP-value
MA0002.20.00475
MA0003.10.848
MA0004.10.489
MA0006.10.0826
MA0007.10.322
MA0009.10.878
MA0014.10.944
MA0017.10.405
MA0018.21.50384e-4
MA0019.10.906
MA0024.10.316
MA0025.10.0364
MA0027.10.489
MA0028.10.727
MA0029.10.208
MA0030.10.0398
MA0031.10.138
MA0035.20.882
MA0038.10.0205
MA0039.20.0775
MA0040.10.67
MA0041.10.45
MA0042.10.613
MA0043.11.23922e-4
MA0046.10.0232
MA0047.20.704
MA0048.10.0181
MA0050.10.0018
MA0051.12.41696e-4
MA0052.10.376
MA0055.10.0575
MA0057.10.622
MA0058.10.222
MA0059.10.13
MA0060.10.00313
MA0061.10.00546
MA0062.20.349
MA0065.20.143
MA0066.10.398
MA0067.10.0625
MA0068.10.552
MA0069.10.237
MA0070.10.0268
MA0071.10.549
MA0072.10.502
MA0073.10.818
MA0074.10.344
MA0076.10.0222
MA0077.12.58949e-6
MA0078.10.027
MA0079.20.0416
MA0080.20.202
MA0081.10.711
MA0083.10.145
MA0084.10.0273
MA0087.10.0238
MA0088.10.581
MA0090.10.366
MA0091.10.81
MA0092.10.249
MA0093.10.55
MA0099.24.71749e-5
MA0100.10.293
MA0101.19.62151e-8
MA0102.20.467
MA0103.10.984
MA0104.20.93
MA0105.12.27157e-4
MA0106.10.0105
MA0107.17.93742e-7
MA0108.20.346
MA0111.10.858
MA0112.20.314
MA0113.10.655
MA0114.10.652
MA0115.10.565
MA0116.10.078
MA0117.10.478
MA0119.10.00549
MA0122.10.983
MA0124.10.997
MA0125.10.447
MA0131.10.189
MA0135.10.0174
MA0136.10.184
MA0137.20.821
MA0138.20.256
MA0139.10.258
MA0140.10.838
MA0141.10.889
MA0142.10.94
MA0143.10.528
MA0144.10.12
MA0145.10.723
MA0146.10.823
MA0147.10.791
MA0148.10.632
MA0149.10.0398
MA0150.10.185
MA0152.10.316
MA0153.10.0724
MA0154.10.198
MA0155.10.993
MA0156.10.974
MA0157.10.767
MA0159.10.234
MA0160.10.105
MA0162.10.0498
MA0163.10.00492
MA0164.10.526
MA0258.10.185
MA0259.10.572



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: CNhs13276

Novel motifP-value
10.0945
100.197
1000.00886
1010.201
1020.939
1030.503
1040.934
1050.112
1060.0487
1070.104
1080.118
1090.179
110.281
1100.0106
1110.0417
1120.609
1130.502
1140.151
1150.844
1160.588
1170.0835
1180.481
1190.0712
120.491
1200.199
1210.605
1220.0921
1230.218
1240.00354
1250.256
1260.928
1270.136
1280.977
1290.714
130.00853
1300.17
1310.259
1320.324
1330.586
1340.3
1350.543
1360.224
1370.318
1380.362
1390.332
140.782
1400.803
1410.0665
1420.419
1430.71
1440.358
1450.0373
1460.75
1470.0756
1480.574
1490.505
150.922
1500.137
1510.86
1520.0184
1530.53
1540.334
1550.919
1560.325
1570.0894
1580.228
1590.351
160.504
1600.136
1610.96
1620.874
1630.862
1640.00688
1650.808
1660.625
1670.0614
1680.888
1690.0415
170.25
180.792
190.3
20.436
200.117
210.524
220.635
230.685
240.693
250.445
260.796
270.995
280.339
290.1
30.311
300.0293
310.899
320.786
330.105
340.452
350.318
360.00624
370.0305
380.382
390.689
40.197
400.0136
410.839
420.918
430.77
440.738
450.46
460.349
470.331
480.319
490.875
50.745
500.899
510.984
520.578
530.651
540.809
550.965
560.805
570.136
580.37
590.86
60.895
600.872
610.555
620.489
630.274
640.795
650.838
660.482
670.55
680.272
690.774
70.772
700.22
710.127
720.736
730.00135
740.586
750.106
760.0437
770.43
780.0191
790.163
80.0047
800.0639
810.968
820.264
830.808
840.94
850.634
860.987
870.37
880.892
890.514
90.199
900.0779
910.548
920.148
930.545
940.724
950.0229
960.915
970.717
980.772
990.112



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: CNhs13276


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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