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{{f5samples
{{f5samples
|id=FF:10025-101D7
|ancestors_in_anatomy_facet=UBERON:0000042,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000077,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000945,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002095,UBERON:0002100,UBERON:0002106,UBERON:0002193,UBERON:0002323,UBERON:0002390,UBERON:0002405,UBERON:0002417,UBERON:0002532,UBERON:0002553,UBERON:0003081,UBERON:0003104,UBERON:0003281,UBERON:0004119,UBERON:0004120,UBERON:0004177,UBERON:0004185,UBERON:0004457,UBERON:0004458,UBERON:0004782,UBERON:0004854,UBERON:0004872,UBERON:0004921,UBERON:0004923,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0005602,UBERON:0006293,UBERON:0007023,UBERON:0007026,UBERON:0009034,UBERON:0009142
|name=spleen, adult, pool1
|sample_id=10025
|rna_tube_id=101D7
|rna_box=101
|rna_position=D7
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Ambion
|rna_lot_number=0910061 -16
|rna_catalog_number=Cat:AM6000 Lot:0910061 -16
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=39,50,70 years old adult
|sample_tissue=spleen
|sample_donor(cell lot)=3 pool
|sample_sex=male
|sample_age=
|sample_ethnicity=mixed
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=normal
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_weight_ug=10
|rna_concentration=1
|sample_note=
|profile_hcage=CNhs10631,LSID657,release008,COMPLETED
|profile_cagescan=NCig10022,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
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|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
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|def=
|fonse_cell_line=
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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:10025-101D7
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010025
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010025
|name=spleen, adult, pool1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=NCig10022,,,
|profile_hcage=CNhs10631,LSID657,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=101
|rna_catalog_number=Cat:AM6000 Lot:0910061 -16
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_lot_number=0910061 -16
|rna_od260/230=
|rna_od260/280=
|rna_position=D7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=101D7
|rna_weight_ug=10
|sample_age=
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Ambion
|sample_description=
|sample_dev_stage=39,50,70 years old adult
|sample_disease=normal
|sample_donor(cell lot)=3 pool
|sample_ethnicity=mixed
|sample_experimental_condition=
|sample_id=10025
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=spleen
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}}
}}

Revision as of 14:00, 21 March 2012


Name:spleen, adult, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespleen
dev stage39,50,70 years old adult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0910061 -16
catalog numberCat:AM6000 Lot:0910061 -16
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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
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C82-Basophils-CD14-Eosinophils-Natural-Peripheral-immature-CD340
C83-choriocarcinoma-pancreatic-placenta-chorionic-HES3GFP-testicular-amniotic0
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-Whole0.0748
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-Whole0.139
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: CNhs10631

Jaspar motifP-value
MA0002.21.46071e-6
MA0003.10.09
MA0004.10.615
MA0006.10.197
MA0007.10.683
MA0009.10.8
MA0014.10.212
MA0017.10.069
MA0018.20.00277
MA0019.10.1
MA0024.10.283
MA0025.10.719
MA0027.10.664
MA0028.10.237
MA0029.10.258
MA0030.10.124
MA0031.10.195
MA0035.20.57
MA0038.10.944
MA0039.20.189
MA0040.10.442
MA0041.10.871
MA0042.10.181
MA0043.10.0206
MA0046.10.952
MA0047.20.437
MA0048.10.00491
MA0050.14.16268e-16
MA0051.11.70694e-8
MA0052.10.662
MA0055.13.7871e-4
MA0057.10.376
MA0058.10.774
MA0059.10.0645
MA0060.10.0176
MA0061.10.276
MA0062.20.061
MA0065.20.814
MA0066.10.745
MA0067.10.196
MA0068.18.1309e-4
MA0069.10.581
MA0070.10.867
MA0071.10.153
MA0072.10.0397
MA0073.10.348
MA0074.10.849
MA0076.10.561
MA0077.10.939
MA0078.10.573
MA0079.20.0344
MA0080.22.19034e-17
MA0081.13.14293e-4
MA0083.10.952
MA0084.10.674
MA0087.10.0972
MA0088.10.369
MA0090.10.4
MA0091.10.385
MA0092.10.657
MA0093.10.6
MA0099.22.23448e-15
MA0100.10.421
MA0101.10.404
MA0102.20.0732
MA0103.10.707
MA0104.20.00993
MA0105.10.776
MA0106.10.00655
MA0107.10.312
MA0108.20.404
MA0111.10.691
MA0112.20.156
MA0113.10.165
MA0114.10.928
MA0115.10.76
MA0116.10.116
MA0117.10.212
MA0119.10.183
MA0122.10.226
MA0124.10.856
MA0125.10.97
MA0131.10.211
MA0135.10.411
MA0136.11.75377e-18
MA0137.24.61317e-7
MA0138.20.166
MA0139.10.59
MA0140.10.786
MA0141.10.98
MA0142.10.513
MA0143.10.518
MA0144.16.57754e-5
MA0145.10.209
MA0146.10.914
MA0147.10.0172
MA0148.10.84
MA0149.10.743
MA0150.10.00541
MA0152.10.379
MA0153.10.31
MA0154.10.0321
MA0155.10.108
MA0156.13.67267e-21
MA0157.10.252
MA0159.10.967
MA0160.10.93
MA0162.10.868
MA0163.10.419
MA0164.10.445
MA0258.10.762
MA0259.10.009



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: CNhs10631

Novel motifP-value
10.323
100.226
1000.0699
1010.974
1020.756
1030.963
1040.634
1050.198
1060.0948
1070.107
1080.644
1090.735
110.921
1100.63
1110.891
1120.154
1130.0692
1140.426
1150.698
1160.131
1170.164
1180.156
1190.993
120.925
1200.331
1210.0579
1220.0957
1230.867
1240.108
1250.782
1260.529
1270.491
1280.55
1290.0233
130.0374
1300.402
1310.884
1320.719
1330.00161
1340.313
1350.00398
1360.73
1370.126
1380.147
1390.636
140.333
1400.612
1410.828
1420.424
1430.0664
1440.749
1450.297
1460.477
1470.213
1480.361
1490.342
150.639
1500.916
1510.948
1520.166
1530.532
1540.366
1550.355
1560.779
1570.228
1580.824
1590.358
160.641
1600.447
1610.82
1620.491
1630.418
1640.0199
1650.852
1660.653
1670.0218
1685.53779e-4
1690.274
170.957
180.494
190.202
20.0229
200.0573
210.569
220.328
230.347
240.373
250.79
260.615
270.0193
280.855
290.205
30.901
300.14
310.509
320.43
330.807
340.0366
350.797
360.756
370.58
380.592
390.742
40.146
400.559
410.767
420.748
430.639
440.531
450.0678
460.788
470.547
480.768
490.933
50.9
500.26
510.536
520.414
530.268
540.524
550.299
560.913
570.0592
580.23
590.0655
60.416
600.416
610.525
620.511
630.838
640.515
650.514
660.119
670.75
680.923
690.219
70.936
700.0531
710.427
720.0166
730.773
740.602
750.233
760.257
770.253
780.928
790.782
80.971
809.55431e-6
810.586
820.416
830.117
840.302
850.407
860.263
870.667
880.351
890.864
90.0495
900.909
910.614
920.409
930.362
940.94
950.517
960.783
970.802
980.305
990.986



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: CNhs10631


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

UBERON: Anatomy
0000042 (serous membrane)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000464 (anatomical space)
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)
0000945 (stomach)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002095 (mesentery)
0002100 (trunk)
0002106 (spleen)
0002193 (hemolymphoid system)
0002323 (body cavity)
0002390 (hematopoietic system)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003281 (mesentery of stomach)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004457 (cavity lining)
0004458 (body cavity or lining)
0004782 (gastrointestinal system serosa)
0004854 (gastrointestinal system mesentery)
0004872 (splanchnic layer of lateral plate mesoderm)
0004921 (subdivision of digestive tract)
0004923 (organ component layer)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0005602 (dorsal mesogastrium)
0006293 (spleen primordium)
0007023 (adult organism)
0007026 (primitive gut)
0009034 (stomach region)
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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