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{{f5samples
{{f5samples
|id=FF:11618-122A7
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|name=Mesenchymal Stem Cells - hepatic, donor2
|sample_id=11618
|rna_tube_id=122A7
|rna_box=122
|rna_position=A7
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=Sciencell/3H
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|rna_catalog_number=SC7525
|sample_species=Human (Homo sapiens)
|sample_strain=
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|sample_sex=
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|rna_od260/280=
|sample_cell_type=mesenchymal stem cell
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_weight_ug=10
|rna_concentration=0.384
|sample_note=
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002195,CL:0002320,CL:0002371,CL:0002571
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002195,CL:0002320,CL:0002371,CL:0002571
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|ancestors_in_disease_facet=
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|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11618-122A7
|is_a=EFO:0002091;;FF:0000002;;FF:0000098;;FF:0000210
|is_a=EFO:0002091;;FF:0000002;;FF:0000098;;FF:0000210
|name=Mesenchymal Stem Cells - hepatic, donor2
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12730,LSID960,release012,COMPLETED
|profile_rnaseq=,,,
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|rna_box=122
|rna_catalog_number=SC7525
|rna_concentration=0.384
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_lot_number=2460
|rna_od260/230=
|rna_od260/280=
|rna_position=A7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=122A7
|rna_weight_ug=10
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=mesenchymal stem cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Sciencell/3H
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11618
|sample_note=
|sample_sex=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=liver
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}}
}}

Revision as of 14:58, 21 March 2012


Name:Mesenchymal Stem Cells - hepatic, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2460
catalog numberSC7525
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





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
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C84-choriocarcinoma-pancreatic-Wilms-Mallassezderived-thymus-salivary-colon0
C85-neuroblastoma-carcinoid-retinoblastoma-small-pineal-rhabdomyosarcoma-medulloblastoma0
C86-colon-carcinoid-small-neuroectodermal-giant-large-neuroepithelioma0
C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
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
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: CNhs12730

Jaspar motifP-value
MA0002.20.0755
MA0003.10.731
MA0004.10.00504
MA0006.10.89
MA0007.10.0486
MA0009.10.934
MA0014.10.53
MA0017.10.421
MA0018.20.0102
MA0019.10.378
MA0024.12.97177e-4
MA0025.10.0105
MA0027.10.611
MA0028.10.00319
MA0029.10.329
MA0030.10.998
MA0031.10.456
MA0035.20.633
MA0038.10.865
MA0039.20.0195
MA0040.10.0168
MA0041.10.662
MA0042.10.284
MA0043.10.294
MA0046.10.514
MA0047.20.95
MA0048.10.148
MA0050.10.00758
MA0051.10.00609
MA0052.10.219
MA0055.10.909
MA0057.10.89
MA0058.14.85137e-4
MA0059.10.0793
MA0060.10.00365
MA0061.10.0435
MA0062.21.59895e-13
MA0065.20.853
MA0066.10.369
MA0067.10.0961
MA0068.10.269
MA0069.10.2
MA0070.10.438
MA0071.10.428
MA0072.10.717
MA0073.10.233
MA0074.10.483
MA0076.11.24394e-6
MA0077.10.217
MA0078.10.835
MA0079.20.197
MA0080.26.22075e-10
MA0081.10.00118
MA0083.13.3023e-7
MA0084.10.102
MA0087.10.207
MA0088.10.879
MA0090.11.73366e-6
MA0091.10.00485
MA0092.10.0202
MA0093.10.00824
MA0099.26.76742e-5
MA0100.10.472
MA0101.10.00306
MA0102.20.512
MA0103.13.06149e-4
MA0104.20.0217
MA0105.10.36
MA0106.10.976
MA0107.10.0017
MA0108.28.38459e-4
MA0111.10.826
MA0112.20.0264
MA0113.10.0145
MA0114.10.852
MA0115.10.0257
MA0116.10.234
MA0117.10.975
MA0119.18.37147e-4
MA0122.10.546
MA0124.10.495
MA0125.10.721
MA0131.10.652
MA0135.10.0115
MA0136.18.16308e-10
MA0137.20.512
MA0138.20.984
MA0139.10.833
MA0140.10.781
MA0141.10.481
MA0142.10.0218
MA0143.10.469
MA0144.10.979
MA0145.10.0417
MA0146.10.144
MA0147.10.0377
MA0148.10.411
MA0149.10.577
MA0150.10.199
MA0152.10.0631
MA0153.10.96
MA0154.10.63
MA0155.10.463
MA0156.12.80454e-12
MA0157.10.724
MA0159.10.818
MA0160.10.179
MA0162.10.238
MA0163.10.105
MA0164.10.708
MA0258.10.298
MA0259.10.69



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: CNhs12730

Novel motifP-value
10.878
100.864
1000.275
1010.967
1020.05
1030.179
1040.547
1050.914
1060.262
1070.0899
1080.962
1090.45
110.777
1100.959
1110.618
1120.895
1130.109
1140.438
1150.264
1160.19
1170.474
1180.535
1190.878
120.326
1200.674
1210.243
1220.0151
1230.0353
1240.644
1250.118
1260.844
1270.709
1280.302
1290.255
130.534
1300.11
1310.204
1320.218
1330.454
1340.32
1350.574
1360.844
1370.143
1380.29
1390.287
140.419
1400.161
1410.371
1420.411
1430.713
1440.383
1450.768
1460.873
1470.123
1480.871
1493.84817e-4
150.267
1500.405
1510.647
1520.126
1530.472
1540.69
1550.207
1560.26
1570.292
1580.967
1590.161
160.0219
1600.34
1610.565
1620.0951
1630.0367
1640.058
1650.897
1660.0811
1670.258
1680.637
1690.0185
170.888
180.493
190.00388
20.249
200.622
210.167
220.0488
230.184
240.446
250.0595
260.815
270.825
280.0732
290.324
30.62
300.629
310.279
327.30905e-16
330.863
340.656
350.454
360.369
370.599
380.514
390.449
40.478
400.708
410.0197
420.546
430.557
440.956
450.863
460.547
470.827
480.761
490.348
50.468
500.349
510.4
520.955
530.123
540.857
550.727
560.879
570.855
580.468
590.667
60.973
600.854
610.821
620.814
630.439
640.738
650.394
660.355
670.404
680.77
690.139
70.526
700.642
710.194
720.883
730.363
740.552
750.95
760.538
770.141
780.809
790.0262
80.255
800.113
810.71
820.802
830.359
840.121
850.0175
860.722
870.0308
880.118
890.427
90.437
900.824
910.81
920.239
930.153
940.652
950.929
960.654
970.573
980.343
990.0214



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: CNhs12730


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002195 (hepatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002571 (hepatic mesenchymal stem cell)

UBERON: Anatomy
0000015 (anatomical boundary)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002384 (connective tissue)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

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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