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FF:11491-119E6: 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 16:44, 29 March 2012


Name:Pericytes, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typepericyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC1205
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-0.107
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-0.465
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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
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: CNhs11317

Jaspar motifP-value
MA0002.20.636
MA0003.10.277
MA0004.10.301
MA0006.10.417
MA0007.10.321
MA0009.10.487
MA0014.10.766
MA0017.10.207
MA0018.20.0838
MA0019.10.0155
MA0024.11.19751e-4
MA0025.10.48
MA0027.10.919
MA0028.10.0675
MA0029.10.477
MA0030.10.807
MA0031.10.342
MA0035.20.87
MA0038.10.181
MA0039.20.533
MA0040.10.159
MA0041.10.196
MA0042.10.512
MA0043.10.00211
MA0046.10.0287
MA0047.20.6
MA0048.10.892
MA0050.10.0158
MA0051.10.0166
MA0052.10.372
MA0055.10.253
MA0057.10.674
MA0058.10.27
MA0059.10.558
MA0060.10.7
MA0061.10.907
MA0062.21.86241e-4
MA0065.20.116
MA0066.10.356
MA0067.10.218
MA0068.10.427
MA0069.10.259
MA0070.10.0516
MA0071.10.124
MA0072.10.733
MA0073.10.791
MA0074.10.305
MA0076.10.0157
MA0077.10.582
MA0078.10.928
MA0079.20.263
MA0080.21.61087e-5
MA0081.10.0709
MA0083.11.39795e-4
MA0084.10.879
MA0087.10.605
MA0088.10.7
MA0090.10.13
MA0091.10.00278
MA0092.10.798
MA0093.10.377
MA0099.20.559
MA0100.10.111
MA0101.10.112
MA0102.20.00272
MA0103.10.814
MA0104.20.439
MA0105.10.962
MA0106.10.967
MA0107.10.196
MA0108.25.3957e-4
MA0111.10.133
MA0112.20.0327
MA0113.10.115
MA0114.10.236
MA0115.10.892
MA0116.10.531
MA0117.10.217
MA0119.10.499
MA0122.10.762
MA0124.10.604
MA0125.10.374
MA0131.10.267
MA0135.10.0622
MA0136.12.34838e-7
MA0137.20.956
MA0138.20.277
MA0139.10.371
MA0140.10.596
MA0141.10.111
MA0142.10.276
MA0143.10.69
MA0144.10.867
MA0145.10.331
MA0146.10.00903
MA0147.10.338
MA0148.10.403
MA0149.10.135
MA0150.10.268
MA0152.10.545
MA0153.10.151
MA0154.10.106
MA0155.10.024
MA0156.12.35679e-6
MA0157.10.195
MA0159.10.668
MA0160.10.561
MA0162.10.165
MA0163.10.228
MA0164.10.43
MA0258.10.0762
MA0259.10.522



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: CNhs11317

Novel motifP-value
10.41
100.16
1000.985
1010.445
1020.674
1030.913
1040.342
1050.0966
1060.317
1070.0904
1080.805
1090.12
110.206
1100.236
1110.575
1120.715
1130.0648
1140.937
1150.287
1160.235
1170.785
1180.834
1190.959
120.505
1200.322
1210.847
1220.372
1232.10785e-4
1240.544
1250.157
1260.733
1270.592
1280.376
1290.562
130.918
1300.468
1310.904
1320.131
1330.577
1340.251
1350.633
1360.83
1370.0342
1380.435
1390.855
140.789
1400.206
1410.165
1420.83
1430.324
1440.843
1450.472
1460.332
1470.38
1480.559
1490.0849
150.167
1500.628
1510.722
1520.203
1530.0639
1540.0424
1550.86
1560.629
1570.334
1580.979
1590.692
160.386
1600.0753
1610.728
1620.173
1630.621
1640.327
1650.125
1660.66
1670.188
1680.998
1690.0591
170.329
180.357
190.0843
20.167
200.732
210.802
220.0424
230.481
240.724
250.308
260.606
270.266
280.129
290.771
30.909
300.0311
310.401
322.70785e-8
330.969
340.0581
350.768
360.246
370.367
380.618
390.592
40.816
400.187
410.247
420.779
430.699
440.72
450.151
460.685
470.895
480.412
490.707
50.505
500.366
510.391
520.539
530.331
540.368
550.698
560.369
570.499
580.242
590.0156
60.387
600.451
610.906
620.295
630.746
640.328
650.061
660.872
670.754
680.187
690.134
70.971
700.664
710.898
720.57
730.121
740.152
750.818
760.293
770.0105
780.769
790.0163
80.395
800.538
810.412
820.221
830.487
840.312
850.159
860.93
870.924
880.268
890.265
90.0838
900.0187
910.335
920.998
930.709
940.936
950.518
960.616
970.388
980.462
990.0139



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: CNhs11317


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)
0000183 (contractile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000630 (supportive cell)
0000669 (pericyte cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002575 (central nervous system pericyte)

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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