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FF:11310-117C5: 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 16:59, 29 March 2012


Name:CD14+ monocyte derived endothelial progenitor cells, donor2
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 stage57 years old adult
sexfemale
age57
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 numberEPC723
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-0.17
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-0.287
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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-Whole0.217
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: CNhs11897

Jaspar motifP-value
MA0002.21.11722e-8
MA0003.10.106
MA0004.10.147
MA0006.10.747
MA0007.10.0752
MA0009.10.214
MA0014.10.29
MA0017.12.02755e-4
MA0018.25.15247e-4
MA0019.10.547
MA0024.10.0275
MA0025.10.682
MA0027.10.491
MA0028.10.322
MA0029.10.961
MA0030.10.473
MA0031.10.427
MA0035.20.815
MA0038.10.116
MA0039.20.177
MA0040.10.642
MA0041.10.519
MA0042.10.903
MA0043.10.0095
MA0046.10.353
MA0047.20.253
MA0048.10.101
MA0050.19.11354e-8
MA0051.10.00205
MA0052.10.0273
MA0055.10.12
MA0057.10.753
MA0058.10.0123
MA0059.10.489
MA0060.12.42459e-5
MA0061.10.202
MA0062.25.1975e-6
MA0065.20.00536
MA0066.10.102
MA0067.10.102
MA0068.10.529
MA0069.10.722
MA0070.10.0548
MA0071.10.328
MA0072.10.895
MA0073.10.572
MA0074.10.213
MA0076.10.214
MA0077.10.472
MA0078.10.531
MA0079.20.231
MA0080.29.66993e-18
MA0081.11.7069e-4
MA0083.17.86475e-4
MA0084.10.281
MA0087.10.259
MA0088.10.219
MA0090.10.00502
MA0091.10.486
MA0092.10.936
MA0093.10.138
MA0099.20.0633
MA0100.10.964
MA0101.10.892
MA0102.20.00611
MA0103.10.309
MA0104.20.674
MA0105.10.0184
MA0106.10.249
MA0107.10.933
MA0108.22.29542e-9
MA0111.10.255
MA0112.20.00111
MA0113.10.157
MA0114.10.00727
MA0115.10.43
MA0116.11.08113e-4
MA0117.10.875
MA0119.10.954
MA0122.10.231
MA0124.10.492
MA0125.10.726
MA0131.10.48
MA0135.10.24
MA0136.17.4252e-18
MA0137.20.0521
MA0138.20.837
MA0139.10.554
MA0140.10.741
MA0141.10.138
MA0142.10.302
MA0143.10.247
MA0144.10.0484
MA0145.10.374
MA0146.10.0101
MA0147.10.923
MA0148.10.859
MA0149.10.122
MA0150.10.198
MA0152.10.361
MA0153.10.206
MA0154.10.00134
MA0155.10.881
MA0156.12.61788e-12
MA0157.10.117
MA0159.10.0246
MA0160.10.0349
MA0162.10.794
MA0163.13.4419e-6
MA0164.10.635
MA0258.10.00334
MA0259.10.462



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: CNhs11897

Novel motifP-value
10.159
100.024
1000.869
1010.238
1020.836
1030.109
1040.952
1050.254
1060.135
1070.49
1080.815
1090.081
110.0887
1100.342
1110.013
1120.236
1130.722
1140.0597
1150.21
1160.881
1170.02
1180.354
1190.078
120.449
1200.414
1210.909
1220.72
1230.0486
1240.146
1250.628
1260.134
1270.111
1280.119
1290.904
130.102
1300.585
1310.303
1320.889
1330.949
1340.595
1350.0678
1360.867
1370.0177
1380.0434
1390.0293
140.167
1400.482
1410.424
1420.185
1430.121
1440.445
1450.278
1460.52
1470.145
1480.025
1490.806
150.162
1500.577
1510.762
1520.389
1530.698
1540.833
1550.0747
1560.567
1570.741
1580.545
1590.215
160.342
1600.649
1610.296
1620.68
1630.313
1640.29
1650.305
1660.261
1670.609
1680.143
1690.016
170.385
180.535
190.387
20.801
200.966
210.273
220.178
230.465
240.0518
250.359
260.152
270.0574
280.549
290.245
30.0214
300.857
310.494
320.813
330.644
340.276
350.32
360.155
370.142
380.153
390.833
40.882
400.19
410.203
420.396
430.0983
440.362
450.536
460.283
470.372
480.244
490.128
50.21
500.844
510.635
520.378
530.175
540.525
550.0248
560.741
570.65
580.0931
590.176
60.367
600.0829
610.131
620.124
630.375
640.292
650.162
660.917
670.315
680.485
690.938
70.138
700.0216
710.0374
720.227
730.0802
740.845
750.0214
760.332
770.448
780.127
790.468
80.179
800.0461
810.223
820.0689
830.952
840.566
850.0799
860.0235
870.125
880.267
890.497
90.299
900.0202
910.865
920.046
930.896
940.139
950.284
960.218
970.967
980.552
990.55



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: CNhs11897


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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