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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005569
|DRA_sample_Accession=CAGE@SAMD00005569
|accession_numbers=CAGE;DRX008518;DRR009390;DRZ000815;DRZ002200
|accession_numbers=CAGE;DRX008518;DRR009390;DRZ000815;DRZ002200;DRZ012165;DRZ013550
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0002320,CL:0000066,CL:0002371,CL:0000213,CL:0002078,CL:0000499,CL:0000153,CL:0000327,CL:0000447,CL:0000215,CL:0000255,CL:0000214
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0002320,CL:0000066,CL:0002371,CL:0000213,CL:0002078,CL:0000499,CL:0000153,CL:0000327,CL:0000447,CL:0000215,CL:0000255,CL:0000214
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|profile_rnaseq=
|profile_rnaseq=
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|profile_srnaseq=SRhi10004,,,
|refex=http://refex.dbcls.jp/genelist.php?lang=en&db=human&roku_valid=1&rk[]=&order_key=score
|refex=http://refex.dbcls.jp/genelist.php?lang
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Revision as of 20:35, 10 August 2017

Name:Synoviocyte, donor3
Species:Human (Homo sapiens)
Library ID:CNhs12050
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7, 8, 9, 10
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesynovium
dev stage61 years old adult
sexmale
age61
cell typesynovial cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2540
catalog numberCA408-R10a
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005569
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12050 CAGE DRX008518 DRR009390
Accession ID Hg19

Library idBAMCTSS
CNhs12050 DRZ000815 DRZ002200
Accession ID Hg38

Library idBAMCTSS
CNhs12050 DRZ012165 DRZ013550
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload


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-penis0.235
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-0.324
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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
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



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: CNhs12050

Jaspar motifP-value
MA0002.20.102
MA0003.10.22
MA0004.10.156
MA0006.10.329
MA0007.10.684
MA0009.10.803
MA0014.10.306
MA0017.10.355
MA0018.23.29475e-5
MA0019.10.999
MA0024.11.09187e-4
MA0025.10.00719
MA0027.10.916
MA0028.10.00437
MA0029.10.499
MA0030.10.0659
MA0031.10.465
MA0035.20.153
MA0038.15.06239e-4
MA0039.20.0329
MA0040.10.79
MA0041.10.935
MA0042.10.473
MA0043.14.06828e-4
MA0046.10.00348
MA0047.20.485
MA0048.10.143
MA0050.10.414
MA0051.10.344
MA0052.10.0857
MA0055.10.922
MA0057.10.29
MA0058.10.0749
MA0059.10.494
MA0060.15.20979e-19
MA0061.10.606
MA0062.21.29664e-9
MA0065.20.479
MA0066.10.986
MA0067.10.0317
MA0068.10.108
MA0069.10.197
MA0070.10.99
MA0071.10.337
MA0072.10.271
MA0073.10.885
MA0074.10.136
MA0076.12.50076e-4
MA0077.10.0463
MA0078.10.895
MA0079.20.78
MA0080.29.10965e-8
MA0081.10.00107
MA0083.10.273
MA0084.10.397
MA0087.10.239
MA0088.10.643
MA0090.10.00395
MA0091.10.143
MA0092.10.467
MA0093.10.101
MA0099.23.99725e-8
MA0100.10.075
MA0101.10.282
MA0102.20.858
MA0103.10.0412
MA0104.20.0594
MA0105.10.72
MA0106.10.16
MA0107.10.695
MA0108.20.956
MA0111.10.655
MA0112.20.00655
MA0113.10.53
MA0114.10.441
MA0115.10.768
MA0116.10.0148
MA0117.10.0988
MA0119.10.168
MA0122.10.66
MA0124.10.2
MA0125.10.0059
MA0131.10.254
MA0135.10.193
MA0136.14.55614e-11
MA0137.20.718
MA0138.20.203
MA0139.10.691
MA0140.10.104
MA0141.10.0254
MA0142.10.0116
MA0143.10.324
MA0144.10.769
MA0145.10.323
MA0146.10.143
MA0147.10.0938
MA0148.10.542
MA0149.10.545
MA0150.10.0243
MA0152.10.0474
MA0153.10.632
MA0154.10.211
MA0155.10.2
MA0156.16.62252e-13
MA0157.10.914
MA0159.10.0389
MA0160.10.976
MA0162.10.0282
MA0163.10.00412
MA0164.10.658
MA0258.10.208
MA0259.10.0706



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: CNhs12050

Novel motifP-value
10.603
100.221
1000.6
1010.729
1020.0406
1030.44
1040.926
1050.0903
1060.457
1070.206
1080.111
1090.473
110.231
1100.205
1110.455
1120.293
1130.261
1140.119
1150.0344
1160.0108
1170.913
1180.48
1190.444
120.169
1200.746
1210.0505
1220.00742
1230.103
1240.395
1250.824
1260.498
1270.772
1280.174
1290.879
130.628
1300.205
1310.41
1320.0759
1330.179
1340.604
1350.676
1360.631
1370.318
1380.742
1390.125
140.633
1400.966
1410.973
1420.617
1430.76
1440.143
1450.368
1460.474
1470.183
1480.578
1490.00335
150.981
1500.477
1510.323
1520.0897
1530.651
1540.868
1550.877
1560.465
1570.91
1580.0719
1590.992
160.0302
1600.335
1610.977
1620.45
1630.859
1640.00896
1650.737
1660.103
1670.614
1680.177
1690.00518
170.248
180.252
190.00232
20.182
200.681
210.128
220.117
230.211
240.0602
250.389
260.3
270.191
280.23
290.138
30.356
300.377
310.6
322.172e-14
330.848
340.49
350.995
360.0617
370.128
380.911
390.172
40.374
400.559
410.381
420.812
430.343
440.21
450.821
460.384
470.915
480.665
490.72
50.643
500.388
510.662
520.692
530.433
540.545
550.216
560.729
570.903
580.492
590.0516
60.511
600.36
610.636
620.897
630.141
640.918
650.328
660.0113
670.801
680.15
690.869
70.291
700.116
710.341
720.814
730.0513
740.16
750.456
760.459
773.25053e-4
780.191
793.02658e-4
80.0526
800.0637
810.61
820.322
830.0241
840.372
850.0486
860.495
870.795
880.0833
890.0108
90.311
900.339
910.697
920.104
930.723
940.343
950.734
960.673
970.448
980.426
990.023



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: CNhs12050


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)
0000548 (animal cell)
0000151 (secretory cell)
0002320 (connective tissue cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000213 (lining cell)
0002078 (meso-epithelial cell)
0000499 (stromal cell)
0000153 (GAG secreting cell)
0000327 (extracellular matrix secreting cell)
0000447 (carbohydrate secreting cell)
0000215 (barrier cell)
0000255 (eukaryotic cell)
0000214 (synovial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000483 (epithelium)
0002384 (connective tissue)
0000479 (tissue)
0000064 (organ part)
0000062 (organ)
0004120 (mesoderm-derived structure)
0004457 (cavity lining)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0004923 (organ component layer)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0006914 (squamous epithelium)
0004905 (articulation)
0000486 (multilaminar epithelium)
0006915 (stratified squamous epithelium)
0007616 (layer of synovial tissue)
0000042 (serous membrane)
0000982 (skeletal joint)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0002217 (synovial joint)
0002018 (synovial membrane of synovial joint)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0004770 (articular system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000187 (human synovial cell sample)

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
CL:0000134 (mesenchymal cell)
CL:0000222 (mesodermal cell)

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