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{{f5samples
{{f5samples
|id=FF:10420-106C6
|F5samples=
|name=colon carcinoma cell line:COLO-320
|ancestors_in_anatomy_facet=UBERON:0000059,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000077,UBERON:0000160,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001046,UBERON:0001052,UBERON:0001062,UBERON:0001155,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0003104,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004907,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
|sample_id=10420
|rna_tube_id=106C6
|rna_box=106
|rna_position=C6
|sample_cell_lot=
|sample_cell_catalog=RCB1193
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=55 year old adult
|sample_tissue=colon
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=55
|sample_ethnicity=unknown
|rna_rin=
|rna_od260/230=1.64
|rna_od260/280=2.07
|sample_cell_type=unclassifiable
|sample_cell_line=COLO-320
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=colon carcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=59.2795
|rna_concentration=2.37118
|sample_note=machine failed, remainder reloaded, low amount
|profile_hcage=CNhs10737,LSID691,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_anatomy_facet=UBERON:0000059,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000077,UBERON:0000160,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001007,UBERON:0001046,UBERON:0001052,UBERON:0001062,UBERON:0001155,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0003104,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004907,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:305,DOID:3119,DOID:4
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:305,DOID:3119,DOID:4
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0101120,FF:0101532
|fonse_cell_line=FF:0101120,FF:0101532
|fonse_cell_line_closure=FF:0101120,FF:0101532
|fonse_cell_line_closure=FF:0101120,FF:0101532
Line 66: Line 34:
|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:10420-106C6
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102047
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102047
|name=colon carcinoma cell line:COLO-320
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10737,LSID691,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=106
|rna_catalog_number=
|rna_concentration=2.37118
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.64
|rna_od260/280=2.07
|rna_position=C6
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=106C6
|rna_weight_ug=59.2795
|sample_age=55
|sample_cell_catalog=RCB1193
|sample_cell_line=COLO-320
|sample_cell_lot=
|sample_cell_type=unclassifiable
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_dev_stage=55 year old adult
|sample_disease=colon carcinoma
|sample_donor(cell lot)=
|sample_ethnicity=unknown
|sample_experimental_condition=
|sample_id=10420
|sample_note=machine failed, remainder reloaded, low amount
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=colon
|top_motifs=LEF1_TCF7_TCF7L1,2:3.53826628993;VSX1,2:2.66164219037;FOXQ1:2.53607197434;NFY{A,B,C}:2.23532385345;TEF:2.10010085453;PBX1:1.99794037035;NKX2-3_NKX2-5:1.97689240561;NRF1:1.9420634319;BREu{core}:1.87630325615;PDX1:1.74319585479;NKX6-1,2:1.72881655855;ZNF143:1.70725791503;PAX8:1.69594560509;E2F1..5:1.64751053712;ADNP_IRX_SIX_ZHX:1.55449713845;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.51508691988;AHR_ARNT_ARNT2:1.49302726441;bHLH_family:1.40575007524;YY1:1.34468392179;FOXN1:1.32844327621;CRX:1.29692979861;RBPJ:1.2937253827;NKX2-1,4:1.262133676;POU3F1..4:1.25327387293;ARID5B:1.22223715458;PAX3,7:1.21939881864;EN1,2:1.20588744286;ELK1,4_GABP{A,B1}:1.12381326484;ZFP161:1.12374398686;FOXA2:1.10342164362;HBP1_HMGB_SSRP1_UBTF:1.03287086218;PITX1..3:0.958099684538;FOX{I1,J2}:0.94154155863;HOXA9_MEIS1:0.927127980825;GFI1:0.913122585783;ALX1:0.910476331777;CDX1,2,4:0.827018912501;MYB:0.814804398648;HOX{A6,A7,B6,B7}:0.806389516773;TOPORS:0.761184244165;NR6A1:0.745190208031;TFDP1:0.729826235533;EVI1:0.704061571189;HOX{A5,B5}:0.699806717267;XBP1:0.600581559933;SOX17:0.586432831681;STAT1,3:0.573935113795;POU1F1:0.571014704521;FOXM1:0.562337495169;NANOG:0.534423381934;STAT5{A,B}:0.526984380336;CREB1:0.515206457935;PAX4:0.500790386917;GATA6:0.460045607102;CUX2:0.457609874809;NANOG{mouse}:0.43615358864;MEF2{A,B,C,D}:0.431736028761;AIRE:0.421698336856;RFX2..5_RFXANK_RFXAP:0.402040252364;TGIF1:0.391288144825;SOX{8,9,10}:0.385164427868;PRDM1:0.376682361546;KLF4:0.375237885964;SNAI1..3:0.374842837385;PPARG:0.372662911419;ZEB1:0.366278300865;BPTF:0.359147796139;POU2F1..3:0.344753428713;GATA4:0.331010201537;CDC5L:0.316754342669;OCT4_SOX2{dimer}:0.314644249414;HES1:0.307746522496;AR:0.302451540413;FOX{D1,D2}:0.28136764393;NR5A1,2:0.26687907373;FOXP1:0.256845507707;POU5F1:0.255352780199;RFX1:0.239213716663;HIF1A:0.218422545226;PRRX1,2:0.191579907619;ZBTB16:0.187883611054;LHX3,4:0.187577518461;IKZF1:0.185819216769;ESRRA:0.14645565542;ZIC1..3:0.125454904035;MYOD1:0.108392789099;T:0.0904552276818;GTF2I:0.0889239456495;LMO2:0.0699428406322;ONECUT1,2:0.068376591127;HAND1,2:0.054147192319;RORA:0.0465360210853;ATF5_CREB3:0.0458073933148;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.045360691967;SOX2:0.0395360581626;ATF4:0.0379604828059;DBP:-0.00303755273579;MYBL2:-0.0228598714444;MZF1:-0.046995713051;IKZF2:-0.0488261430524;HNF1A:-0.0589880621325;RREB1:-0.0745585080068;PAX2:-0.0832789969085;SP1:-0.0885244483575;SREBF1,2:-0.101416045098;GFI1B:-0.104996837824;HNF4A_NR2F1,2:-0.107447011131;MED-1{core}:-0.1252733284;ELF1,2,4:-0.132779161356;NHLH1,2:-0.167063220066;PAX6:-0.167740618189;HOX{A4,D4}:-0.172367457283;POU6F1:-0.17926069617;FOXP3:-0.185986263764;HMGA1,2:-0.188443216436;GTF2A1,2:-0.199165540711;TFAP2{A,C}:-0.222542988601;HIC1:-0.228476767197;PAX1,9:-0.235026639226;MYFfamily:-0.248531644474;FOX{F1,F2,J1}:-0.256036333258;PAX5:-0.26205738234;ZBTB6:-0.272487591217;NFIL3:-0.273692055173;FOSL2:-0.28454948874;ATF6:-0.290358481329;HLF:-0.294005915821;ATF2:-0.345767432355;NFKB1_REL_RELA:-0.388864102978;TLX2:-0.392862552777;PATZ1:-0.394322392166;TAL1_TCF{3,4,12}:-0.402438970131;SOX5:-0.413271409937;IRF7:-0.428344098919;NKX3-2:-0.429264394255;NFIX:-0.434123333347;DMAP1_NCOR{1,2}_SMARC:-0.445863932635;RUNX1..3:-0.453894259164;TFAP2B:-0.496598492936;EGR1..3:-0.505985881542;FOS_FOS{B,L1}_JUN{B,D}:-0.509879953172;TFAP4:-0.511286027919;CEBPA,B_DDIT3:-0.521092737271;FOXD3:-0.577759125777;SPIB:-0.590301819918;UFEwm:-0.606153948448;NFE2L2:-0.618826125846;NFE2:-0.648360225642;NKX3-1:-0.651458935667;TEAD1:-0.6582657243;SPI1:-0.677010496589;BACH2:-0.67876172525;MTE{core}:-0.686190252323;REST:-0.697045677559;EBF1:-0.702839472783;FOXO1,3,4:-0.733758792535;ZNF384:-0.750141047978;JUN:-0.794941540529;TLX1..3_NFIC{dimer}:-0.839500441447;GCM1,2:-0.84570382142;NR3C1:-0.876156120504;NKX2-2,8:-0.892557325888;SMAD1..7,9:-0.937885039573;NFATC1..3:-0.966986640434;TBP:-0.978430767268;XCPE1{core}:-0.99620127631;MAFB:-0.99785527233;IRF1,2:-1.00734321065;FOXL1:-1.0127587303;ETS1,2:-1.01903136134;ZNF238:-1.05885099662;MTF1:-1.06546871332;ALX4:-1.06795764866;GZF1:-1.07284555336;MAZ:-1.08865474516;RXR{A,B,G}:-1.09698949431;HSF1,2:-1.11850391887;TP53:-1.15754937655;ZNF148:-1.18982100179;NR1H4:-1.34380987574;ESR1:-1.34756386002;TBX4,5:-1.46169677784;GLI1..3:-1.51703278451;NFE2L1:-1.5783418277;SRF:-1.58839028171;RXRA_VDR{dimer}:-1.60277761184;STAT2,4,6:-1.62781881598;SPZ1:-1.79771536599;HMX1:-1.9341548219;EP300:-2.12562833946;TFCP2:-2.13000104565;ZNF423:-2.14639859329
}}
}}

Revision as of 14:06, 21 March 2012


Name:colon carcinoma cell line:COLO-320
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecolon
dev stage55 year old adult
sexfemale
age55
cell typeunclassifiable
cell lineCOLO-320
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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]





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-0.0221
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-lymphoma0.6
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs10737

Jaspar motifP-value
MA0002.20.00203
MA0003.10.23
MA0004.10.0443
MA0006.10.122
MA0007.10.52
MA0009.10.993
MA0014.10.947
MA0017.10.0286
MA0018.20.185
MA0019.10.659
MA0024.13.30143e-5
MA0025.10.149
MA0027.10.109
MA0028.10.0222
MA0029.10.768
MA0030.10.932
MA0031.10.426
MA0035.20.706
MA0038.13.71289e-5
MA0039.20.835
MA0040.10.701
MA0041.10.279
MA0042.10.476
MA0043.10.0055
MA0046.10.923
MA0047.20.816
MA0048.10.35
MA0050.11.80614e-8
MA0051.10.00939
MA0052.10.375
MA0055.10.136
MA0057.10.114
MA0058.10.014
MA0059.10.0402
MA0060.14.00892e-19
MA0061.10.0585
MA0062.20.0418
MA0065.20.151
MA0066.10.261
MA0067.10.692
MA0068.10.0298
MA0069.10.515
MA0070.10.106
MA0071.10.977
MA0072.10.805
MA0073.10.565
MA0074.10.331
MA0076.10.00329
MA0077.10.652
MA0078.10.158
MA0079.20.318
MA0080.24.82585e-10
MA0081.10.041
MA0083.19.77903e-6
MA0084.10.55
MA0087.10.178
MA0088.10.0316
MA0090.10.102
MA0091.10.125
MA0092.10.0266
MA0093.10.0169
MA0099.28.87205e-15
MA0100.10.188
MA0101.10.254
MA0102.20.0127
MA0103.10.785
MA0104.20.00168
MA0105.10.0691
MA0106.10.189
MA0107.10.0689
MA0108.20.0199
MA0111.10.929
MA0112.20.00239
MA0113.10.531
MA0114.10.408
MA0115.10.838
MA0116.10.0707
MA0117.10.712
MA0119.10.35
MA0122.10.667
MA0124.10.78
MA0125.10.0596
MA0131.10.317
MA0135.10.109
MA0136.11.82122e-6
MA0137.20.058
MA0138.20.216
MA0139.10.383
MA0140.10.505
MA0141.10.926
MA0142.10.0585
MA0143.10.998
MA0144.10.00614
MA0145.10.0445
MA0146.10.126
MA0147.10.00273
MA0148.10.57
MA0149.10.238
MA0150.10.00487
MA0152.10.765
MA0153.10.576
MA0154.10.0313
MA0155.10.135
MA0156.10.014
MA0157.10.588
MA0159.10.204
MA0160.10.518
MA0162.10.169
MA0163.10.0594
MA0164.10.984
MA0258.10.0471
MA0259.10.0202



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: CNhs10737

Novel motifP-value
10.705
100.751
1000.871
1010.733
1020.694
1030.358
1040.616
1050.845
1062.29208e-5
1070.0147
1080.669
1090.172
110.159
1100.552
1110.39
1120.0544
1130.18
1140.0914
1150.246
1160.508
1170.839
1180.764
1190.157
120.53
1200.571
1210.764
1220.527
1230.807
1240.909
1250.899
1260.946
1270.652
1280.0252
1290.666
130.904
1300.708
1310.0226
1320.718
1330.752
1340.855
1350.0125
1360.885
1370.223
1380.165
1390.0886
140.4
1400.721
1410.215
1420.41
1430.063
1440.831
1450.189
1460.922
1470.535
1480.074
1490.0476
150.66
1500.295
1510.186
1520.00952
1530.535
1540.972
1550.947
1560.973
1570.444
1580.892
1590.777
160.289
1600.568
1610.744
1620.517
1630.71
1640.946
1650.216
1660.667
1670.159
1680.27
1690.0217
170.15
180.287
190.115
20.202
200.345
210.414
220.153
230.00381
240.756
250.587
260.295
270.113
280.949
290.99
30.312
300.277
310.495
320.0043
330.812
340.214
350.793
360.511
370.0561
380.57
390.224
40.511
400.718
410.351
420.877
430.0977
440.106
450.322
460.184
470.831
480.457
490.263
50.23
500.546
510.769
520.115
530.523
540.421
550.0282
560.378
570.729
580.355
590.0142
60.43
600.0146
610.937
620.221
630.113
640.814
650.0299
660.04
670.861
680.933
690.157
70.999
700.0261
710.319
720.204
730.0163
740.672
750.837
760.445
770.0577
780.966
790.0265
80.325
800.364
810.456
820.0229
830.384
840.258
850.00888
860.602
870.642
880.859
890.0818
90.109
900.288
910.0217
920.181
930.163
940.0309
950.189
960.25
970.817
980.635
990.563



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: CNhs10737


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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
299 (adenocarcinoma)
305 (carcinoma)
3119 (gastrointestinal system cancer)
4 (disease)

UBERON: Anatomy
0000059 (large intestine)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001046 (hindgut)
0001052 (rectum)
0001062 (anatomical entity)
0001155 (colon)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004907 (lower digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
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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