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{{f5samples
{{f5samples
|id=FF:10603-108E9
|F5samples=
|name=embryonic pancreas cell line:2C6
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000160,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001045,UBERON:0001048,UBERON:0001062,UBERON:0001264,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002108,UBERON:0002114,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003921,UBERON:0003922,UBERON:0003923,UBERON:0003924,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004458,UBERON:0004921,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
|sample_id=10603
|rna_tube_id=108E9
|rna_box=108
|rna_position=E9
|sample_cell_lot=
|sample_cell_catalog=RCB0794
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=pancreas
|sample_donor(cell lot)=
|sample_sex=unknown
|sample_age=19 week embryo
|sample_ethnicity=J
|rna_rin=
|rna_od260/230=2.08
|rna_od260/280=2.17
|sample_cell_type=unclassifiable
|sample_cell_line=2C6
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=36.59749
|rna_concentration=0.77867
|sample_note=
|profile_hcage=CNhs11814,LSID829,release010,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000160,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001045,UBERON:0001048,UBERON:0001062,UBERON:0001264,UBERON:0001555,UBERON:0002050,UBERON:0002075,UBERON:0002100,UBERON:0002108,UBERON:0002114,UBERON:0002323,UBERON:0002532,UBERON:0002553,UBERON:0003104,UBERON:0003921,UBERON:0003922,UBERON:0003923,UBERON:0003924,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004458,UBERON:0004921,UBERON:0005177,UBERON:0005409,UBERON:0005423,UBERON:0007026,UBERON:0009142
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0100669
|fonse_cell_line=FF:0100669
|fonse_cell_line_closure=FF:0100669
|fonse_cell_line_closure=FF:0100669
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:10603-108E9
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100669;;UBERON:0001264
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100669;;UBERON:0001264
|name=embryonic pancreas cell line:2C6
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11814,LSID829,release010,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=108
|rna_catalog_number=
|rna_concentration=0.77867
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.08
|rna_od260/280=2.17
|rna_position=E9
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=108E9
|rna_weight_ug=36.59749
|sample_age=19 week embryo
|sample_cell_catalog=RCB0794
|sample_cell_line=2C6
|sample_cell_lot=
|sample_cell_type=unclassifiable
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_experimental_condition=
|sample_id=10603
|sample_note=
|sample_sex=unknown
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=pancreas
|top_motifs=FOXQ1:2.34089613867;PAX8:1.59787344818;RORA:1.1750863936;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.16498918786;POU1F1:1.15258191936;RBPJ:0.980318502177;ONECUT1,2:0.893879372681;bHLH_family:0.854518545106;FOX{F1,F2,J1}:0.853841189314;PAX1,9:0.847008321051;POU6F1:0.814186854527;NANOG:0.812235474758;ALX1:0.802702673266;FOX{I1,J2}:0.793982633285;STAT5{A,B}:0.742904589309;FOXD3:0.677852369026;PDX1:0.673001845384;GLI1..3:0.583689877324;CEBPA,B_DDIT3:0.574381803696;ADNP_IRX_SIX_ZHX:0.550516944813;NFE2L2:0.53887873772;PAX4:0.521699869747;BPTF:0.519679540127;E2F1..5:0.513472482583;VSX1,2:0.503477906876;EGR1..3:0.485826514528;BREu{core}:0.47003553196;NFIX:0.46553159524;LEF1_TCF7_TCF7L1,2:0.46530344005;PRRX1,2:0.462234255831;RXR{A,B,G}:0.437950917335;FOS_FOS{B,L1}_JUN{B,D}:0.435207159563;HOX{A5,B5}:0.416474062662;OCT4_SOX2{dimer}:0.411644290463;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.411274541738;TFAP2B:0.399685550516;FOXA2:0.383718057002;TFAP2{A,C}:0.380030545049;NKX2-1,4:0.374352067433;SOX17:0.354619778225;POU5F1:0.346186328206;NR5A1,2:0.32167418885;LHX3,4:0.306539031687;ZNF423:0.293518239695;RXRA_VDR{dimer}:0.288790151858;ZNF143:0.287407623452;TLX1..3_NFIC{dimer}:0.27144178393;NR3C1:0.270910411902;NFE2:0.261996999376;ZFP161:0.261691202045;ZNF148:0.258096016323;NFIL3:0.253061010446;GATA6:0.248312837199;NR1H4:0.21859281061;HES1:0.214606974752;HOX{A6,A7,B6,B7}:0.205999564053;NRF1:0.204881423804;PITX1..3:0.195198132483;AHR_ARNT_ARNT2:0.190393239172;TBX4,5:0.181202340361;NR6A1:0.178623835529;XCPE1{core}:0.178623789224;BACH2:0.172432071215;ATF4:0.169445289223;PAX5:0.168295597228;TP53:0.166163388272;ELK1,4_GABP{A,B1}:0.1538063492;HNF4A_NR2F1,2:0.145938743441;HLF:0.130878303677;CUX2:0.128944749518;RFX1:0.125257692421;MYB:0.110035178189;EN1,2:0.106619214341;HNF1A:0.0919620213198;CDC5L:0.0909850614541;MYOD1:0.0853883731232;FOSL2:0.0623083828374;AIRE:0.0598319455756;ESR1:0.057554249649;NFKB1_REL_RELA:0.0228689771179;TFDP1:0.0216308020781;IRF7:0.00631240969645;NKX3-1:0.00413087198326;HIC1:-0.00474281735581;SNAI1..3:-0.00663945216411;IKZF2:-0.0111159557028;TEAD1:-0.0190512282886;PRDM1:-0.0268103543939;ZBTB16:-0.0335955952235;YY1:-0.0343723367453;PATZ1:-0.0392388422065;POU2F1..3:-0.0564594177945;FOXP1:-0.0642959228415;SOX5:-0.078065705041;REST:-0.0797420613352;SP1:-0.091286078729;PAX2:-0.096911285239;ETS1,2:-0.103084185274;T:-0.10824262657;ZEB1:-0.111216203428;TEF:-0.113044695391;TAL1_TCF{3,4,12}:-0.114040152911;GTF2I:-0.114043636264;PBX1:-0.118110608241;GTF2A1,2:-0.11834611812;SOX{8,9,10}:-0.123262049961;MED-1{core}:-0.131106005188;FOX{D1,D2}:-0.156419393762;HOXA9_MEIS1:-0.166209694785;ATF2:-0.181575124389;ELF1,2,4:-0.190227444917;ZBTB6:-0.191512535953;MTF1:-0.200885016895;PAX3,7:-0.22432905634;PPARG:-0.232298995395;AR:-0.240760612637;HOX{A4,D4}:-0.242975291751;MEF2{A,B,C,D}:-0.250335461883;NKX2-3_NKX2-5:-0.252604366258;SPIB:-0.255991621196;TFAP4:-0.260046090282;TFCP2:-0.27005707131;NFY{A,B,C}:-0.28085643803;NHLH1,2:-0.28966236094;LMO2:-0.293491225813;DMAP1_NCOR{1,2}_SMARC:-0.296511459401;XBP1:-0.306593713194;NKX2-2,8:-0.315569905143;POU3F1..4:-0.32002618054;GFI1:-0.32343351782;IKZF1:-0.339337619306;SOX2:-0.366435949595;HAND1,2:-0.383627501359;SPI1:-0.389218558972;RUNX1..3:-0.417241346798;ATF5_CREB3:-0.418126755128;NFATC1..3:-0.420550357761;GZF1:-0.436308391121;RREB1:-0.450365596384;FOXL1:-0.478078662164;RFX2..5_RFXANK_RFXAP:-0.47965212974;MAZ:-0.509744999444;EBF1:-0.521937188515;STAT2,4,6:-0.526045694555;JUN:-0.534903969287;SRF:-0.542026127418;CRX:-0.548871782053;TOPORS:-0.555017261684;SMAD1..7,9:-0.556027381403;FOXM1:-0.576970143904;ESRRA:-0.588305205972;CDX1,2,4:-0.594348920676;ZNF238:-0.60470432322;ZNF384:-0.643842713625;IRF1,2:-0.67779945029;HMGA1,2:-0.698387822357;PAX6:-0.704914359341;MYBL2:-0.718589193277;GFI1B:-0.722187983045;ZIC1..3:-0.724072820958;CREB1:-0.755586565961;SREBF1,2:-0.759486646018;FOXO1,3,4:-0.771266142245;UFEwm:-0.778742290307;HBP1_HMGB_SSRP1_UBTF:-0.791633096893;MZF1:-0.798953256309;ARID5B:-0.80644830762;NKX3-2:-0.822001240174;MTE{core}:-0.824878334534;EVI1:-0.840603426298;DBP:-0.89039736508;ALX4:-0.897272705494;HSF1,2:-0.907623779788;MYFfamily:-0.926375429678;NKX6-1,2:-0.955230450185;TBP:-0.956668940032;KLF4:-0.97593943271;NFE2L1:-0.979512269427;NANOG{mouse}:-1.00538708946;MAFB:-1.02483343386;GATA4:-1.04236944154;STAT1,3:-1.11104525963;FOXN1:-1.13367506383;SPZ1:-1.15550453389;TGIF1:-1.18489071858;FOXP3:-1.32255470604;TLX2:-1.34586539555;EP300:-1.365738399;HIF1A:-1.40803711443;HMX1:-1.43110334727;ATF6:-1.59154530508;GCM1,2:-1.67307935001
}}
}}

Revision as of 14:11, 21 March 2012


Name:embryonic pancreas cell line:2C6
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuepancreas
dev stageNA
sexunknown
age19 week embryo
cell typeunclassifiable
cell line2C6
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-0.115
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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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 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: CNhs11814

Jaspar motifP-value
MA0002.20.292
MA0003.10.52
MA0004.10.0105
MA0006.10.976
MA0007.10.433
MA0009.10.326
MA0014.10.397
MA0017.10.0327
MA0018.20.317
MA0019.10.6
MA0024.10.0523
MA0025.10.608
MA0027.10.508
MA0028.10.19
MA0029.10.106
MA0030.10.0171
MA0031.10.525
MA0035.20.00759
MA0038.10.682
MA0039.20.0231
MA0040.10.233
MA0041.10.2
MA0042.10.472
MA0043.10.743
MA0046.10.0627
MA0047.20.0681
MA0048.10.0346
MA0050.10.0701
MA0051.10.839
MA0052.10.128
MA0055.11.89298e-4
MA0057.10.673
MA0058.10.0453
MA0059.10.135
MA0060.10.805
MA0061.10.131
MA0062.20.753
MA0065.20.00103
MA0066.10.784
MA0067.10.693
MA0068.10.362
MA0069.10.63
MA0070.10.769
MA0071.10.238
MA0072.10.124
MA0073.10.753
MA0074.10.877
MA0076.10.744
MA0077.10.716
MA0078.10.551
MA0079.20.539
MA0080.20.302
MA0081.10.671
MA0083.10.254
MA0084.10.395
MA0087.10.668
MA0088.10.173
MA0090.10.393
MA0091.10.155
MA0092.10.197
MA0093.10.0326
MA0099.24.32089e-14
MA0100.10.93
MA0101.10.0861
MA0102.20.309
MA0103.10.134
MA0104.20.00747
MA0105.10.699
MA0106.10.351
MA0107.10.0825
MA0108.20.0149
MA0111.10.304
MA0112.20.679
MA0113.10.375
MA0114.10.0045
MA0115.10.11
MA0116.10.255
MA0117.10.128
MA0119.10.0167
MA0122.10.0648
MA0124.10.401
MA0125.10.728
MA0131.10.0144
MA0135.10.425
MA0136.10.922
MA0137.20.545
MA0138.20.762
MA0139.10.675
MA0140.10.00261
MA0141.10.176
MA0142.10.343
MA0143.10.997
MA0144.10.751
MA0145.10.36
MA0146.10.668
MA0147.18.10496e-4
MA0148.10.00399
MA0149.10.0457
MA0150.10.0576
MA0152.10.841
MA0153.10.657
MA0154.10.94
MA0155.10.761
MA0156.10.223
MA0157.10.614
MA0159.10.103
MA0160.10.0361
MA0162.10.216
MA0163.10.139
MA0164.10.802
MA0258.10.697
MA0259.10.467



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: CNhs11814

Novel motifP-value
10.774
100.734
1000.922
1010.83
1020.22
1030.0712
1040.604
1050.0817
1060.0446
1070.476
1080.765
1090.011
110.999
1100.184
1110.0253
1120.342
1130.244
1140.367
1150.319
1160.474
1170.655
1180.882
1190.403
120.518
1200.453
1210.706
1220.0216
1230.304
1240.53
1250.775
1260.982
1270.975
1280.699
1290.239
130.0396
1300.108
1310.0669
1320.627
1330.0224
1340.227
1350.0508
1360.924
1370.586
1380.705
1390.0549
140.21
1400.877
1410.7
1420.915
1430.514
1440.492
1450.411
1460.0786
1470.2
1480.256
1490.66
150.0135
1500.855
1510.585
1520.775
1530.619
1540.688
1550.669
1560.45
1570.406
1580.739
1590.472
160.964
1600.488
1610.215
1620.955
1630.674
1640.52
1650.953
1660.0884
1670.41
1680.819
1690.985
170.177
180.486
190.117
20.871
200.114
210.654
220.319
230.655
240.581
250.477
260.627
270.498
280.245
290.801
30.684
300.823
310.6
320.00421
330.583
340.155
350.635
360.0707
370.204
380.0677
390.732
40.298
400.0393
410.32
420.103
430.633
440.0855
450.0841
460.956
470.866
480.991
490.148
50.471
500.317
510.275
520.369
530.729
540.159
550.254
560.261
570.0385
580.897
590.435
60.393
600.606
610.183
620.588
630.503
640.638
650.396
660.00831
670.693
680.76
690.772
70.212
700.136
710.36
720.455
730.639
740.711
750.68
760.356
770.677
780.804
790.049
80.631
800.241
810.0642
820.185
830.812
840.189
850.237
860.198
870.534
880.631
890.669
90.64
900.387
910.724
920.343
930.693
940.737
950.174
960.953
970.327
980.026
990.588



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: CNhs11814


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
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
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)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001045 (midgut)
0001048 (primordium)
0001062 (anatomical entity)
0001264 (pancreas)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002108 (small intestine)
0002114 (duodenum)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003921 (pancreas primordium)
0003922 (pancreatic epithelial bud)
0003923 (dorsal pancreatic bud)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004921 (subdivision of digestive tract)
0005177 (trunk region element)
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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