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{{f5samples
{{f5samples
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|DRA_sample_Accession=CAGE@SAMD00004733
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|accession_numbers=CAGE;DRX007784;DRR008656;DRZ000081;DRZ001466;DRZ011431;DRZ012816
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
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|fonse_treatment_closure=FF:0000343,FF:0011132,FF:11900-125F1
|fonse_treatment_closure=FF:0000343,FF:0011132,FF:11900-125F1
|has_quality=
|has_quality=
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|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/Hep-2%2520cells%2520mock%2520treated%252c%2520biol_rep3.CNhs13501.11900-125F1.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/Hep-2%2520cells%2520mock%2520treated%252c%2520biol_rep3.CNhs13501.11900-125F1.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/Hep-2%2520cells%2520mock%2520treated%252c%2520biol_rep3.CNhs13501.11900-125F1.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/Hep-2%2520cells%2520mock%2520treated%252c%2520biol_rep3.CNhs13501.11900-125F1.hg38.nobarcode.ctss.bed.gz
|id=FF:11900-125F1
|id=FF:11900-125F1
|is_a=EFO:0002091;;FF:0011132
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|library_id=CNhs13501
|library_id=CNhs13501
|library_id_phase_based=2:CNhs13501
|library_id_phase_based=2:CNhs13501
|microRNAs=
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|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11900
|name=Hep-2 cells mock treated, biol_rep3
|name=Hep-2 cells mock treated, biol_rep3
|namespace=
|namespace=
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|profile_rnaseq=
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Line 91: Line 100:
|top_motifs=FOXQ1:1.70314915325;E2F1..5:1.66299094638;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.63948804651;HES1:1.56356477293;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.53126067273;ESRRA:1.50539882127;NR5A1,2:1.35290148151;HIF1A:1.26893769415;ELK1,4_GABP{A,B1}:1.25633456593;PPARG:1.20042727723;FOXM1:1.03675498638;YY1:0.972858327261;NKX3-1:0.937182072823;NRF1:0.929761483507;PAX1,9:0.880568344106;MYB:0.765614555903;NFY{A,B,C}:0.744969090772;ZNF143:0.721784967346;HNF4A_NR2F1,2:0.68672587967;bHLH_family:0.659689915977;FOXD3:0.656328827379;NKX3-2:0.633379533568;VSX1,2:0.630330868835;FOXN1:0.622543294486;POU1F1:0.622303247161;GCM1,2:0.60873637823;TFDP1:0.581879894525;SNAI1..3:0.578936814548;HOXA9_MEIS1:0.551562057063;HOX{A6,A7,B6,B7}:0.548186627343;PAX5:0.519547201298;TEAD1:0.497210729354;PAX8:0.446008171913;TEF:0.425364816936;ZEB1:0.423712746462;IKZF2:0.410799993745;NR6A1:0.401820331102;EP300:0.37842648442;GFI1:0.368626673092;IRF7:0.342103831552;ZNF148:0.341780883251;MYOD1:0.316811658611;UFEwm:0.295454351492;PITX1..3:0.283677561525;TBX4,5:0.271291185744;IKZF1:0.269699906731;CREB1:0.266603901115;BREu{core}:0.237105780333;HOX{A5,B5}:0.191235285871;NFE2L1:0.189031978249;TP53:0.188181787055;GZF1:0.1843838857;CUX2:0.177968364677;FOX{F1,F2,J1}:0.175895472428;MYBL2:0.1409067932;SOX{8,9,10}:0.127783222748;LEF1_TCF7_TCF7L1,2:0.125075443584;ARID5B:0.122923581524;HSF1,2:0.109389758177;MTF1:0.102489604139;LHX3,4:0.0955531060958;PDX1:0.0773662873933;HAND1,2:0.0531393394399;AHR_ARNT_ARNT2:0.0333407663383;ZBTB16:0.0326490999313;HNF1A:0.0150173745874;NFE2:0.00658397532707;ALX4:0.00620061131982;FOX{I1,J2}:0.00332483661509;NR1H4:0.00283465308369;RXR{A,B,G}:-0.0142489139866;PAX2:-0.0175041009898;PRRX1,2:-0.021308035711;GLI1..3:-0.0223150215819;HLF:-0.0249488550272;EN1,2:-0.0264022031429;OCT4_SOX2{dimer}:-0.0356179401656;PAX3,7:-0.0393543287154;NFE2L2:-0.0430288000567;BACH2:-0.0530283665822;POU3F1..4:-0.0547924810745;PAX4:-0.0551694830593;NKX2-2,8:-0.0568236803203;ATF5_CREB3:-0.0736239815588;ADNP_IRX_SIX_ZHX:-0.076485392698;ONECUT1,2:-0.0787238176146;STAT5{A,B}:-0.082918946355;PBX1:-0.083266954683;DBP:-0.0842011363457;FOXL1:-0.0855438103494;RORA:-0.0907382378939;FOS_FOS{B,L1}_JUN{B,D}:-0.101710687665;CRX:-0.131116111791;ATF4:-0.134706151864;ZNF384:-0.135776356345;RFX2..5_RFXANK_RFXAP:-0.13785401562;HOX{A4,D4}:-0.13892095906;KLF4:-0.146720881093;GTF2A1,2:-0.166760214945;NR3C1:-0.178309370657;CDX1,2,4:-0.182138506533;GFI1B:-0.20405807913;POU2F1..3:-0.210384137041;MEF2{A,B,C,D}:-0.212582534352;BPTF:-0.214298079958;NKX6-1,2:-0.227533672106;NFIL3:-0.229759033861;TFCP2:-0.237876428951;CEBPA,B_DDIT3:-0.248133462516;ZNF423:-0.249606921744;TLX1..3_NFIC{dimer}:-0.269646870944;CDC5L:-0.270710456523;HBP1_HMGB_SSRP1_UBTF:-0.279364282801;T:-0.291276899341;TBP:-0.307361158764;POU6F1:-0.313380206997;PAX6:-0.320944723377;ELF1,2,4:-0.348708039185;LMO2:-0.349054452482;ZBTB6:-0.349717028285;AIRE:-0.349880438524;FOSL2:-0.371805101659;ATF6:-0.372739941668;NFKB1_REL_RELA:-0.380408195352;ZFP161:-0.382687397709;EBF1:-0.383457511261;HIC1:-0.403768016387;NANOG:-0.409693325137;IRF1,2:-0.420106029843;TFAP2{A,C}:-0.421785528289;SREBF1,2:-0.426729105721;ESR1:-0.434972082498;ALX1:-0.435065593336;HMGA1,2:-0.456918088621;RBPJ:-0.481170577116;RFX1:-0.493696854708;FOXA2:-0.494075048907;SOX2:-0.520935463368;AR:-0.524672240944;GATA6:-0.530890484402;FOXP1:-0.534165341961;SPIB:-0.534930497308;TFAP2B:-0.561994194219;GTF2I:-0.572915013308;STAT2,4,6:-0.581592031375;JUN:-0.613411899111;REST:-0.622173491705;FOXP3:-0.631484657163;SOX5:-0.634991435437;NKX2-3_NKX2-5:-0.635942913053;NFIX:-0.641537513397;SPI1:-0.646329019697;NKX2-1,4:-0.650254749755;MED-1{core}:-0.653861624781;RUNX1..3:-0.658431935727;SOX17:-0.661341381952;MAFB:-0.663749732376;EVI1:-0.664719980143;POU5F1:-0.670408823747;MTE{core}:-0.677647508544;SP1:-0.67788460193;ZIC1..3:-0.687729242229;NFATC1..3:-0.692062085183;EGR1..3:-0.712497701561;DMAP1_NCOR{1,2}_SMARC:-0.724211635845;GATA4:-0.739687123489;ETS1,2:-0.763564170108;NHLH1,2:-0.772096237179;TAL1_TCF{3,4,12}:-0.828942518238;TFAP4:-0.849096158617;ZNF238:-0.879690095268;MYFfamily:-0.891486144409;SRF:-0.910300168499;TOPORS:-0.932080026499;STAT1,3:-0.939524107005;XCPE1{core}:-0.965272804757;RREB1:-0.975813486733;ATF2:-0.993627520692;RXRA_VDR{dimer}:-0.994928389622;FOX{D1,D2}:-1.01057165054;MAZ:-1.04310537278;PRDM1:-1.04404388926;XBP1:-1.09787509712;MZF1:-1.19940040136;FOXO1,3,4:-1.21342441273;HMX1:-1.21380401205;TGIF1:-1.25201968912;SMAD1..7,9:-1.26078383542;PATZ1:-1.28026323295;TLX2:-1.39225039637;NANOG{mouse}:-1.6581633759;SPZ1:-1.88824163484
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|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11900-125F1;search_select_hide=table117:FF:11900-125F1
}}
}}

Latest revision as of 18:27, 4 June 2020

Name:Hep-2 cells mock treated, biol_rep3
Species:Human (Homo sapiens)
Library ID:CNhs13501
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
age56
cell typeunclassifiable
cell lineHep-2
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3c
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004733
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13501 CAGE DRX007784 DRR008656
Accession ID Hg19

Library idBAMCTSS
CNhs13501 DRZ000081 DRZ001466
Accession ID Hg38

Library idBAMCTSS
CNhs13501 DRZ011431 DRZ012816
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
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.0416
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0.783
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.522
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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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: CNhs13501

Jaspar motifP-value
MA0002.20.0325
MA0003.10.732
MA0004.10.12
MA0006.10.467
MA0007.10.337
MA0009.10.358
MA0014.10.665
MA0017.10.472
MA0018.20.867
MA0019.10.973
MA0024.19.30238e-9
MA0025.10.131
MA0027.10.718
MA0028.16.01047e-6
MA0029.10.761
MA0030.10.437
MA0031.10.088
MA0035.20.519
MA0038.10.882
MA0039.20.031
MA0040.10.552
MA0041.10.366
MA0042.10.565
MA0043.10.148
MA0046.10.657
MA0047.20.933
MA0048.10.0376
MA0050.10.0077
MA0051.10.879
MA0052.10.00132
MA0055.16.56662e-4
MA0057.10.138
MA0058.10.0776
MA0059.10.0132
MA0060.10.0316
MA0061.10.0213
MA0062.20.0105
MA0065.20.0203
MA0066.10.752
MA0067.10.117
MA0068.12.22889e-4
MA0069.10.294
MA0070.10.592
MA0071.10.0357
MA0072.10.567
MA0073.10.274
MA0074.10.64
MA0076.14.58078e-5
MA0077.10.763
MA0078.10.326
MA0079.20.207
MA0080.22.95044e-8
MA0081.10.322
MA0083.12.69877e-4
MA0084.10.235
MA0087.10.535
MA0088.10.0198
MA0090.10.0135
MA0091.10.309
MA0092.10.987
MA0093.10.0792
MA0099.20.0139
MA0100.10.256
MA0101.10.106
MA0102.20.821
MA0103.10.0277
MA0104.25.53782e-4
MA0105.10.21
MA0106.10.912
MA0107.10.0174
MA0108.20.0795
MA0111.10.647
MA0112.20.0964
MA0113.10.912
MA0114.10.0071
MA0115.10.0072
MA0116.10.913
MA0117.10.957
MA0119.10.826
MA0122.10.981
MA0124.11
MA0125.10.319
MA0131.10.2
MA0135.10.538
MA0136.10.00137
MA0137.20.0088
MA0138.20.0525
MA0139.11
MA0140.10.719
MA0141.10.00648
MA0142.10.448
MA0143.10.371
MA0144.10.227
MA0145.10.938
MA0146.10.29
MA0147.13.61021e-4
MA0148.10.167
MA0149.10.036
MA0150.10.505
MA0152.10.692
MA0153.10.0324
MA0154.10.361
MA0155.10.0775
MA0156.10.0676
MA0157.10.0493
MA0159.10.252
MA0160.10.0374
MA0162.10.509
MA0163.10.186
MA0164.10.323
MA0258.10.875
MA0259.10.0175



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: CNhs13501

Novel motifP-value
10.0831
100.112
1000.0347
1010.241
1020.935
1030.92
1040.843
1050.171
1060.00553
1070.0956
1080.538
1090.00147
110.822
1100.652
1110.465
1120.313
1130.00397
1140.429
1150.878
1160.306
1170.241
1180.181
1190.871
120.646
1200.0279
1210.691
1220.162
1230.402
1240.807
1250.846
1260.953
1270.156
1287.33005e-4
1290.321
132.25697e-4
1300.5
1310.203
1320.463
1330.137
1340.966
1350.138
1360.00191
1370.476
1380.702
1390.196
140.365
1400.321
1410.338
1420.511
1430.202
1440.535
1450.125
1460.726
1470.902
1480.408
1490.573
150.63
1500.81
1510.58
1520.232
1530.492
1540.468
1550.288
1560.048
1570.148
1580.237
1590.263
160.849
1600.565
1610.507
1620.851
1630.293
1640.0527
1650.751
1660.0151
1670.165
1680.374
1690.568
170.7
180.195
190.607
20.402
200.147
210.34
220.785
230.00273
240.522
250.15
260.738
270.656
280.798
290.0188
30.475
300.373
310.554
320.0441
330.22
340.157
350.939
360.169
370.699
380.723
390.991
40.443
400.0134
410.201
420.882
430.32
440.0743
450.161
460.539
470.448
480.495
490.254
50.36
500.806
510.619
520.356
530.183
540.408
550.0207
560.82
570.522
580.994
590.711
60.795
600.385
610.0547
620.902
630.538
640.738
650.297
660.31
670.814
680.529
690.542
70.016
700.207
710.047
720.645
730.87
740.143
750.179
760.258
770.713
780.248
790.642
80.107
800.0696
810.395
820.0472
830.822
840.184
850.0228
860.741
870.016
880.707
890.976
90.476
900.0606
910.0125
920.0599
930.197
940.755
950.0493
960.638
970.889
980.725
990.565



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: CNhs13501


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)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
305 (carcinoma)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001737 (larynx)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000072 (segment of respiratory tract)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0001004 (respiratory system)
0001557 (upper respiratory tract)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000343 (control treatment sample)
0000350 (experimentally modified sample)
0104978 (HEp-2 cell sample)
0100297 (carcinoma cell line sample)
0101120 (epithelial cell line sample)
0011132 (human Hep-2 cells mock treated 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
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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