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FF:11386-118B9: 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:CD14+ monocyte derived endothelial progenitor cells, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stage46 years old adult
sexmale
age46
cell typeblood vessel endothelial progenitor cell
cell lineNA
company3HBiomedical
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberEPC724
catalog number3H100-81-10
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-0.175
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
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-Whole0.0995
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: CNhs11904

Jaspar motifP-value
MA0002.23.89423e-5
MA0003.10.204
MA0004.10.116
MA0006.10.704
MA0007.10.0719
MA0009.10.0852
MA0014.10.481
MA0017.12.6241e-4
MA0018.27.31345e-4
MA0019.10.648
MA0024.10.00458
MA0025.10.905
MA0027.10.526
MA0028.10.176
MA0029.10.716
MA0030.10.585
MA0031.10.269
MA0035.20.854
MA0038.10.209
MA0039.20.475
MA0040.10.638
MA0041.10.507
MA0042.10.753
MA0043.10.0157
MA0046.10.863
MA0047.20.0286
MA0048.10.154
MA0050.14.14589e-7
MA0051.10.0166
MA0052.10.0263
MA0055.10.214
MA0057.10.926
MA0058.10.00442
MA0059.10.731
MA0060.13.19107e-6
MA0061.10.184
MA0062.24.43869e-6
MA0065.20.0252
MA0066.10.168
MA0067.10.122
MA0068.10.297
MA0069.10.634
MA0070.10.0671
MA0071.10.192
MA0072.10.715
MA0073.10.396
MA0074.10.144
MA0076.10.167
MA0077.10.486
MA0078.10.646
MA0079.20.0279
MA0080.23.60226e-18
MA0081.11.18292e-4
MA0083.13.37209e-4
MA0084.10.301
MA0087.10.342
MA0088.10.34
MA0090.10.0145
MA0091.10.173
MA0092.10.998
MA0093.10.104
MA0099.20.218
MA0100.10.986
MA0101.10.745
MA0102.20.00121
MA0103.10.828
MA0104.20.953
MA0105.10.0424
MA0106.10.223
MA0107.10.824
MA0108.23.32226e-11
MA0111.10.186
MA0112.20.00205
MA0113.10.141
MA0114.10.00876
MA0115.10.628
MA0116.11.78979e-4
MA0117.10.706
MA0119.10.931
MA0122.10.496
MA0124.10.255
MA0125.10.459
MA0131.10.355
MA0135.10.192
MA0136.15.77955e-16
MA0137.20.00766
MA0138.20.971
MA0139.10.85
MA0140.10.984
MA0141.10.0327
MA0142.10.146
MA0143.10.0535
MA0144.10.0116
MA0145.10.22
MA0146.10.0362
MA0147.10.452
MA0148.10.396
MA0149.10.285
MA0150.10.0794
MA0152.10.389
MA0153.10.167
MA0154.10.00223
MA0155.10.924
MA0156.15.19765e-11
MA0157.10.0655
MA0159.10.0551
MA0160.10.0301
MA0162.10.795
MA0163.12.31129e-5
MA0164.10.597
MA0258.10.00383
MA0259.10.186



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: CNhs11904

Novel motifP-value
10.198
100.0453
1000.738
1010.257
1020.714
1030.103
1040.93
1050.39
1060.136
1070.533
1080.862
1090.114
110.144
1100.46
1110.0434
1120.415
1130.823
1140.0451
1150.139
1160.968
1170.0199
1180.426
1190.0378
120.442
1200.431
1210.884
1220.253
1230.041
1240.234
1250.345
1260.0789
1270.11
1280.0883
1290.957
130.0916
1300.872
1310.476
1320.695
1330.986
1340.565
1350.342
1360.726
1370.00869
1380.103
1390.0421
140.133
1400.0922
1410.619
1420.215
1430.454
1440.31
1450.402
1460.896
1470.216
1480.0249
1490.745
150.24
1500.467
1510.803
1520.634
1530.615
1540.84
1550.264
1560.84
1570.38
1580.654
1590.21
160.345
1600.99
1610.331
1620.538
1630.548
1640.207
1650.159
1660.477
1670.578
1680.294
1690.0588
170.382
180.572
190.255
20.761
200.955
210.447
220.126
230.456
240.0331
250.461
260.114
270.132
280.49
290.323
30.0173
300.703
310.346
320.86
330.851
340.268
350.332
360.251
370.185
380.103
390.886
40.827
400.314
410.144
420.353
430.1
440.67
450.448
460.199
470.517
480.295
490.136
50.2
500.682
510.529
520.275
530.158
540.359
550.0396
560.734
570.596
580.0885
590.116
60.465
600.0792
610.158
620.126
630.344
640.435
650.151
660.841
670.107
680.456
690.878
70.16
700.0393
710.0767
720.264
730.101
740.706
750.0339
760.294
770.286
780.116
790.437
80.273
800.138
810.234
820.0808
830.579
840.785
850.0507
860.0171
870.118
880.253
890.439
90.288
900.0198
910.868
920.0644
930.878
940.111
950.735
960.159
970.801
980.369
990.47



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: CNhs11904


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000066 (epithelial cell)
0000115 (endothelial cell)
0000134 (mesenchymal cell)
0000213 (lining cell)
0000215 (barrier cell)
0000219 (motile cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0002078 (meso-epithelial cell)
0002320 (connective tissue cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002619 (adult endothelial progenitor cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

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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