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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002097,UBERON:0002193,UBERON:0002199,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002416,UBERON:0002532,UBERON:0003102,UBERON:0004120,UBERON:0004765,UBERON:0005423
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000035,CL:0000037,CL:0000040,CL:0000048,CL:0000049,CL:0000054,CL:0000055,CL:0000062,CL:0000063,CL:0000092,CL:0000134,CL:0000137,CL:0000144,CL:0000151,CL:0000219,CL:0000255,CL:0000335,CL:0000375,CL:0000548,CL:0000557,CL:0000559,CL:0000566,CL:0000576,CL:0000723,CL:0000738,CL:0000763,CL:0000766,CL:0000837,CL:0000839,CL:0000988,CL:0001012,CL:0002009,CL:0002031,CL:0002032,CL:0002087,CL:0002092,CL:0002194,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100583,FF:0103765
|fonse_cell_line=FF:0100583,FF:0103765
|fonse_cell_line_closure=FF:0100583,FF:0103765
|fonse_cell_line_closure=FF:0100583,FF:0103765

Revision as of 16:56, 29 March 2012


Name:fibrous histiocytoma cell line:GCT TIB-223
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelung
dev stageNA
sexmale
age29
cell typeunclassifiable
cell lineGCT TIB-223
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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-penis0.362
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-lymphoma0.566
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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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: CNhs11842

Jaspar motifP-value
MA0002.20.152
MA0003.10.122
MA0004.10.0518
MA0006.10.644
MA0007.10.369
MA0009.10.63
MA0014.10.61
MA0017.10.382
MA0018.20.237
MA0019.10.878
MA0024.12.10951e-6
MA0025.10.169
MA0027.10.914
MA0028.12.59524e-15
MA0029.10.86
MA0030.10.0905
MA0031.10.119
MA0035.20.285
MA0038.14.39357e-5
MA0039.20.119
MA0040.10.0969
MA0041.10.282
MA0042.10.468
MA0043.10.0971
MA0046.10.0568
MA0047.20.322
MA0048.10.00102
MA0050.10.449
MA0051.10.188
MA0052.10.132
MA0055.10.00142
MA0057.10.997
MA0058.10.0287
MA0059.10.0154
MA0060.14.22856e-13
MA0061.10.983
MA0062.24.96817e-17
MA0065.20.867
MA0066.10.674
MA0067.10.926
MA0068.10.765
MA0069.10.892
MA0070.10.737
MA0071.10.911
MA0072.10.564
MA0073.10.916
MA0074.10.635
MA0076.11.22373e-18
MA0077.10.947
MA0078.10.259
MA0079.20.0193
MA0080.20.174
MA0081.10.302
MA0083.10.00624
MA0084.10.723
MA0087.10.256
MA0088.11.34694e-6
MA0090.10.723
MA0091.10.0142
MA0092.10.453
MA0093.10.0275
MA0099.26.95335e-12
MA0100.10.0649
MA0101.10.0994
MA0102.20.251
MA0103.10.0268
MA0104.20.00233
MA0105.10.318
MA0106.10.679
MA0107.10.351
MA0108.20.749
MA0111.10.98
MA0112.20.0766
MA0113.10.105
MA0114.10.904
MA0115.10.421
MA0116.10.793
MA0117.10.436
MA0119.10.6
MA0122.10.337
MA0124.10.799
MA0125.10.775
MA0131.10.277
MA0135.10.034
MA0136.10.00281
MA0137.20.942
MA0138.20.21
MA0139.10.949
MA0140.10.915
MA0141.10.746
MA0142.10.476
MA0143.10.446
MA0144.10.573
MA0145.10.164
MA0146.10.0238
MA0147.10.00334
MA0148.10.314
MA0149.10.00509
MA0150.10.275
MA0152.10.287
MA0153.10.00729
MA0154.10.325
MA0155.10.2
MA0156.17.52554e-10
MA0157.10.803
MA0159.10.895
MA0160.10.414
MA0162.10.939
MA0163.10.129
MA0164.10.45
MA0258.10.0681
MA0259.10.0389



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: CNhs11842

Novel motifP-value
10.211
100.117
1000.261
1010.429
1020.423
1030.684
1040.995
1050.354
1060.389
1070.785
1080.965
1090.831
110.675
1100.287
1110.13
1120.215
1130.209
1140.676
1150.397
1160.78
1170.178
1180.786
1190.416
120.838
1200.399
1210.89
1220.771
1230.931
1240.271
1250.304
1260.738
1270.316
1280.17
1290.991
130.106
1300.0676
1310.112
1320.15
1330.109
1340.098
1350.086
1360.0745
1370.673
1380.497
1390.036
140.322
1400.181
1410.974
1420.52
1430.63
1440.788
1450.585
1460.418
1470.684
1480.867
1490.0788
150.72
1500.219
1510.0938
1520.226
1530.178
1540.718
1550.289
1560.917
1570.269
1580.433
1590.143
160.357
1600.681
1610.408
1620.589
1630.992
1640.84
1650.614
1660.28
1670.722
1680.723
1690.0716
170.632
180.929
190.198
20.192
200.275
210.235
220.131
230.011
240.404
250.669
260.13
270.191
280.948
290.212
30.56
300.125
310.258
320.00511
330.508
340.182
350.649
360.205
370.716
380.812
390.32
40.302
400.617
410.264
420.283
430.662
440.918
450.281
460.578
470.372
480.268
490.652
50.129
500.824
510.329
520.0145
530.609
540.31
550.988
560.917
570.388
580.283
590.104
60.233
600.0717
610.533
620.289
630.924
640.755
650.205
669.64945e-6
670.223
680.605
690.138
70.892
700.343
710.675
720.313
730.981
740.31
750.107
760.268
770.507
780.827
790.218
80.419
800.129
810.791
820.0401
830.0402
840.813
850.0385
860.732
870.122
880.711
890.272
90.371
900.466
910.0225
920.162
930.816
940.726
950.423
960.602
970.616
980.673
990.621



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: CNhs11842


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)
0000035 (single fate stem cell)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000054 (bone matrix secreting cell)
0000055 (non-terminally differentiated cell)
0000062 (osteoblast)
0000092 (osteoclast)
0000134 (mesenchymal cell)
0000137 (osteocyte)
0000151 (secretory cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000335 (mesenchyme condensation cell)
0000375 (osteoprogenitor cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002092 (bone marrow cell)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060072 (benign neoplasm)
0060083 (immune system cancer)
0060085 (organ system benign neoplasm)
0060100 (musculoskeletal system cancer)
0060121 (integumentary system benign neoplasm)
14566 (disease of cellular proliferation)
162 (cancer)
200 (giant cell tumor)
201 (connective tissue cancer)
2438 (dermis tumor)
2531 (hematologic cancer)
3165 (skin benign neoplasm)
4 (disease)
4305 (bone giant cell tumor)
4418 (cutaneous fibrous histiocytoma)
7 (disease of anatomical entity)

UBERON: Anatomy
0000014 (zone of skin)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002097 (skin of body)
0002193 (hemolymphoid system)
0002199 (integument)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002416 (integumental system)
0002532 (epiblast (generic))
0003102 (surface structure)
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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