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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005511
|DRA_sample_Accession=CAGE@SAMD00005511
|accession_numbers=CAGE;DRX007862;DRR008734;DRZ000159;DRZ001544
|accession_numbers=CAGE;DRX007862;DRR008734;DRZ000159;DRZ001544;DRZ011509;DRZ012894
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002563,CL:0000255,CL:0002076,CL:0002251,CL:0002253
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002563,CL:0000255,CL:0002076,CL:0002251,CL:0002253
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|fonse_treatment_closure=
|fonse_treatment_closure=
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|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/colon%2520carcinoma%2520cell%2520line%253aCACO-2.CNhs11280.10513-107D9.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/colon%2520carcinoma%2520cell%2520line%253aCACO-2.CNhs11280.10513-107D9.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/colon%2520carcinoma%2520cell%2520line%253aCACO-2.CNhs11280.10513-107D9.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/colon%2520carcinoma%2520cell%2520line%253aCACO-2.CNhs11280.10513-107D9.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/colon%2520carcinoma%2520cell%2520line%253aCACO-2.CNhs11280.10513-107D9.hg38.nobarcode.ctss.bed.gz
|id=FF:10513-107D9
|id=FF:10513-107D9
|is_a=EFO:0002091;;FF:0000210;;FF:0100195
|is_a=EFO:0002091;;FF:0000210;;FF:0100195
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|library_id=CNhs11280
|library_id=CNhs11280
|library_id_phase_based=2:CNhs11280
|library_id_phase_based=2:CNhs11280
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10513
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10513
|name=colon carcinoma cell line:CACO-2
|name=colon carcinoma cell line:CACO-2
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 91: Line 100:
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|top_motifs=HNF1A:3.06583846818;HNF4A_NR2F1,2:2.91576677331;FOXA2:2.07747986817;SNAI1..3:2.06952913165;LEF1_TCF7_TCF7L1,2:1.79040010615;FOX{F1,F2,J1}:1.76022898379;ZEB1:1.74269718529;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.71615833627;NFY{A,B,C}:1.53570490242;E2F1..5:1.41837478945;LHX3,4:1.39993910202;bHLH_family:1.37849117682;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.35279380345;MYOD1:1.25296948779;VSX1,2:1.19991715544;ADNP_IRX_SIX_ZHX:1.16086015688;POU2F1..3:1.04862113891;EN1,2:1.01294232739;TEAD1:0.946914874683;GATA6:0.933321801619;ONECUT1,2:0.822216153487;HOXA9_MEIS1:0.810349558401;HOX{A6,A7,B6,B7}:0.806341855979;ELK1,4_GABP{A,B1}:0.785955332913;SOX{8,9,10}:0.778393844614;SP1:0.772638519403;FOXN1:0.747190812919;TFDP1:0.735156972237;RBPJ:0.733552919442;NKX2-3_NKX2-5:0.722950798524;ESRRA:0.673846886301;XCPE1{core}:0.638734371675;NRF1:0.638598655605;MYB:0.580210974631;ZNF143:0.52702785081;YY1:0.526564839922;TBP:0.523901240541;SOX17:0.478400170866;FOXD3:0.461767807247;PBX1:0.447052962324;TEF:0.43135347902;CRX:0.368269980302;HOX{A5,B5}:0.33621498131;FOXP1:0.31943607684;EVI1:0.318994598676;HLF:0.301832981378;STAT5{A,B}:0.29553786084;ATF4:0.28937184219;FOXQ1:0.283545256825;ZNF148:0.283313465046;OCT4_SOX2{dimer}:0.281472915695;GFI1:0.278520007206;NKX3-2:0.276982677615;FOX{D1,D2}:0.218186571626;ESR1:0.196674332859;RORA:0.190044711457;PDX1:0.168745318429;SREBF1,2:0.159471114464;ARID5B:0.146862548942;DBP:0.134570075321;PITX1..3:0.103947343251;POU5F1:0.100923595552;LMO2:0.0816737187448;HBP1_HMGB_SSRP1_UBTF:0.0750827049814;CUX2:0.0589530466885;PAX8:0.0470893103788;HES1:0.0320343613335;FOX{I1,J2}:0.023139587432;IKZF1:-0.000838371840211;SOX2:-0.0124426186078;FOXM1:-0.0180389661025;NFIX:-0.0254849628228;HAND1,2:-0.0473908801352;TBX4,5:-0.0580215476813;HIC1:-0.0795000754822;MED-1{core}:-0.0884420488624;BREu{core}:-0.0887145722463;POU1F1:-0.0995903458825;HSF1,2:-0.106521882606;POU3F1..4:-0.121769177157;T:-0.15834816474;SOX5:-0.159671534411;PAX3,7:-0.174077762011;MYBL2:-0.182885362853;AIRE:-0.188494900078;ZFP161:-0.19424315104;NFE2:-0.21920837458;IKZF2:-0.232634890621;ATF6:-0.235820115021;PAX1,9:-0.235932258128;SRF:-0.238276570919;FOS_FOS{B,L1}_JUN{B,D}:-0.238307048965;HMGA1,2:-0.23968986481;ELF1,2,4:-0.242980930748;DMAP1_NCOR{1,2}_SMARC:-0.252710507162;STAT2,4,6:-0.253014574581;KLF4:-0.25708806522;RXRA_VDR{dimer}:-0.263723509942;PATZ1:-0.265255366358;PAX2:-0.290065577341;ALX1:-0.303319456354;MAZ:-0.303750883749;NFKB1_REL_RELA:-0.304308666273;TFCP2:-0.312024409668;HOX{A4,D4}:-0.315573988383;ATF5_CREB3:-0.317186072434;NHLH1,2:-0.317730255363;MTE{core}:-0.330728976681;JUN:-0.332545457012;TOPORS:-0.345398426927;BACH2:-0.364829307322;FOXO1,3,4:-0.389148715716;NANOG:-0.39063632366;STAT1,3:-0.394875933164;MEF2{A,B,C,D}:-0.396208805636;CDC5L:-0.400313433754;FOSL2:-0.402394052307;NFE2L2:-0.427805920343;CEBPA,B_DDIT3:-0.430866404003;PAX4:-0.43895561375;NR5A1,2:-0.441369173532;ZIC1..3:-0.457562783779;ATF2:-0.467312088682;POU6F1:-0.473220234091;EBF1:-0.477092160349;RFX1:-0.489926261524;NKX6-1,2:-0.49511326058;UFEwm:-0.498576945403;NFIL3:-0.508014271276;GFI1B:-0.510640909799;RFX2..5_RFXANK_RFXAP:-0.51492023968;ZBTB16:-0.530357114263;TP53:-0.536415909868;PAX5:-0.541878918794;SPZ1:-0.565444814015;REST:-0.566817354689;FOXL1:-0.573785284739;ZBTB6:-0.576722014798;TFAP2B:-0.586709860995;SPIB:-0.605226339396;RXR{A,B,G}:-0.64395262702;CREB1:-0.644092666994;PRRX1,2:-0.645445996758;ZNF384:-0.653076534449;TFAP2{A,C}:-0.657273246429;SPI1:-0.669271244974;AHR_ARNT_ARNT2:-0.679373449813;ALX4:-0.70369868465;RUNX1..3:-0.715834867357;TAL1_TCF{3,4,12}:-0.750973940205;TLX2:-0.757789290895;MYFfamily:-0.771884401669;XBP1:-0.780131644357;TFAP4:-0.819664451107;FOXP3:-0.823749214052;IRF7:-0.825254762743;CDX1,2,4:-0.826842151699;HIF1A:-0.829998782668;EGR1..3:-0.831582359535;PPARG:-0.852619418576;GTF2I:-0.854320001692;PRDM1:-0.875886042068;ETS1,2:-0.876203211598;MZF1:-0.88344617097;GTF2A1,2:-0.901752020242;MAFB:-0.942836489082;ZNF238:-0.965698643315;NR3C1:-1.03927427606;AR:-1.04027615536;MTF1:-1.05433684735;IRF1,2:-1.08569890061;NKX2-2,8:-1.109011404;TGIF1:-1.11945307463;GCM1,2:-1.12727754882;NR6A1:-1.14848222075;BPTF:-1.15424910796;RREB1:-1.22041501536;NANOG{mouse}:-1.31240477302;NKX2-1,4:-1.35453760983;SMAD1..7,9:-1.42512335604;NFATC1..3:-1.43525157531;EP300:-1.44638139183;GZF1:-1.46331443646;TLX1..3_NFIC{dimer}:-1.48605272066;NFE2L1:-1.5218071268;NR1H4:-1.54041743461;ZNF423:-1.54191462268;PAX6:-1.5737320654;GLI1..3:-1.59383092941;GATA4:-1.60991088923;HMX1:-1.61379313342;NKX3-1:-1.83411500716
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10513-107D9;search_select_hide=table117:FF:10513-107D9
}}
}}

Latest revision as of 14:28, 3 June 2020

Name:colon carcinoma cell line:CACO-2
Species:Human (Homo sapiens)
Library ID:CNhs11280
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuecolon
dev stageNA
sexmale
age72
cell typeunclassifiable
cell lineCACO-2
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005511
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11280 CAGE DRX007862 DRR008734
Accession ID Hg19

Library idBAMCTSS
CNhs11280 DRZ000159 DRZ001544
Accession ID Hg38

Library idBAMCTSS
CNhs11280 DRZ011509 DRZ012894
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
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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



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: CNhs11280

Jaspar motifP-value
MA0002.20.00695
MA0003.10.508
MA0004.10.0137
MA0006.10.459
MA0007.10.956
MA0009.10.221
MA0014.10.00681
MA0017.12.56641e-12
MA0018.20.89
MA0019.10.639
MA0024.11.6392e-7
MA0025.10.711
MA0027.10.98
MA0028.10.00833
MA0029.12.9972e-4
MA0030.10.18
MA0031.10.0299
MA0035.29.01544e-7
MA0038.13.44608e-5
MA0039.28.54906e-4
MA0040.10.188
MA0041.10.21
MA0042.10.282
MA0043.10.552
MA0046.15.03016e-61
MA0047.20.00139
MA0048.10.993
MA0050.19.20479e-8
MA0051.10.0134
MA0052.10.0545
MA0055.10.00278
MA0057.10.708
MA0058.10.00286
MA0059.10.0817
MA0060.11.92436e-18
MA0061.16.9769e-5
MA0062.20.0321
MA0065.25.28678e-4
MA0066.10.184
MA0067.10.128
MA0068.10.205
MA0069.10.971
MA0070.10.788
MA0071.10.921
MA0072.10.0329
MA0073.10.6
MA0074.10.79
MA0076.10.0291
MA0077.10.315
MA0078.10.207
MA0079.20.626
MA0080.21.11366e-9
MA0081.10.051
MA0083.10.955
MA0084.10.808
MA0087.10.638
MA0088.10.257
MA0090.10.00341
MA0091.10.0475
MA0092.10.334
MA0093.10.01
MA0099.21.25571e-4
MA0100.10.163
MA0101.10.0183
MA0102.20.725
MA0103.11.15208e-6
MA0104.20.00571
MA0105.12.08005e-4
MA0106.10.295
MA0107.10.00129
MA0108.20.31
MA0111.10.979
MA0112.20.0798
MA0113.10.387
MA0114.13.34743e-17
MA0115.18.46311e-5
MA0116.10.0035
MA0117.10.923
MA0119.10.00115
MA0122.10.978
MA0124.10.467
MA0125.10.0105
MA0131.10.406
MA0135.10.584
MA0136.11.83072e-6
MA0137.20.139
MA0138.20.234
MA0139.10.206
MA0140.11.17482e-5
MA0141.10.622
MA0142.10.106
MA0143.10.381
MA0144.10.124
MA0145.10.201
MA0146.10.902
MA0147.10.0165
MA0148.18.4449e-4
MA0149.10.0987
MA0150.10.0116
MA0152.10.865
MA0153.19.93332e-48
MA0154.10.00537
MA0155.10.414
MA0156.17.36852e-4
MA0157.10.132
MA0159.10.784
MA0160.10.446
MA0162.10.578
MA0163.10.319
MA0164.10.0596
MA0258.10.195
MA0259.10.345



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: CNhs11280

Novel motifP-value
10.667
100.533
1000.278
1010.635
1020.372
1030.892
1040.629
1050.777
1060.0788
1070.498
1080.636
1090.453
110.42
1100.402
1110.881
1120.102
1130.54
1140.289
1150.583
1160.327
1170.81
1180.478
1190.916
120.978
1200.796
1210.392
1220.121
1230.41
1240.287
1250.31
1260.55
1270.413
1280.0522
1290.979
130.00503
1300.0705
1310.165
1320.613
1330.0428
1340.455
1350.204
1360.00648
1370.0964
1380.0331
1390.0302
140.408
1400.741
1410.847
1420.723
1430.0983
1440.409
1450.508
1460.798
1470.512
1480.405
1490.641
150.729
1500.494
1510.208
1520.375
1530.594
1540.0989
1550.349
1560.616
1570.336
1580.363
1590.693
160.724
1600.328
1610.807
1620.956
1630.201
1640.303
1650.818
1660.0431
1670.812
1680.24
1690.488
170.791
180.0277
190.149
20.241
200.418
210.225
220.604
230.0224
240.622
250.886
260.992
270.337
280.876
290.702
30.427
300.654
310.712
320.0128
330.637
340.513
350.391
360.318
370.421
380.815
390.399
40.551
400.0343
410.0492
420.868
430.21
440.596
450.525
460.307
470.542
480.743
490.337
50.623
500.359
510.814
520.932
530.45
540.754
550.566
560.657
570.931
580.637
590.0616
60.84
600.373
610.319
620.25
630.553
640.667
650.0645
662.9958e-4
670.119
680.201
690.387
70.157
700.0944
710.494
720.578
730.604
740.166
750.692
760.947
770.214
780.00764
790.111
80.772
800.22
810.391
820.00826
830.651
840.483
850.0917
860.66
870.0819
880.991
890.0303
90.0469
900.778
910.00516
920.076
930.856
940.025
950.317
960.246
970.924
980.703
990.799



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: CNhs11280


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)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0002253 (epithelial cell of large intestine)

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

UBERON: Anatomy
0000468 (multi-cellular organism)
0001155 (colon)
0001052 (rectum)
0000160 (intestine)
0000483 (epithelium)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0005911 (endo-epithelium)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0000485 (simple columnar epithelium)
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004808 (gastrointestinal system epithelium)
0001277 (intestinal epithelium)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0000059 (large intestine)
0005409 (gastrointestinal system)
0004907 (lower digestive tract)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0101913 (colonic adenocarcinoma cell line sample)
0101120 (epithelial cell line sample)
0100167 (adenocarcinoma cell line sample)
0100797 (colonic cancer cell line)
0101532 (rectal cancer cell line sample)
0101914 (colorectal adenocarcinoma cell line sample)
0101616 (colorectal cancer cell line sample)
0100195 (CACO-2 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:0000223 (endodermal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0010316 (germ layer / neural crest)

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