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{{f5samples
{{f5samples
|id=FF:11872-125B9
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|name=CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor2
|sample_id=11872
|rna_tube_id=125B9
|rna_box=125
|rna_position=B9
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=D4-3
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|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=
|sample_donor(cell lot)=donor2
|sample_sex=male
|sample_age=51
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|rna_rin=8.6
|rna_od260/230=1.47
|rna_od260/280=2.02
|sample_cell_type=monocyte
|sample_cell_line=
|sample_collaboration=Christine Wells (University of Queensland)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=2.767455
|rna_concentration=0.61499
|sample_note=
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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000040,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000557,CL:0000559,CL:0000566,CL:0000576,CL:0000723,CL:0000738,CL:0000763,CL:0000766,CL:0000837,CL:0000839,CL:0000860,CL:0000988,CL:0001012,CL:0002009,CL:0002031,CL:0002032,CL:0002057,CL:0002087,CL:0002194,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000040,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000557,CL:0000559,CL:0000566,CL:0000576,CL:0000723,CL:0000738,CL:0000763,CL:0000766,CL:0000837,CL:0000839,CL:0000860,CL:0000988,CL:0001012,CL:0002009,CL:0002031,CL:0002032,CL:0002057,CL:0002087,CL:0002194,CL:0002320,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002193,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423
|ancestors_in_disease_facet=
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|sample_description=
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|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=EFO:0000369,FF:0000625,FF:0000631,FF:0011444,FF:11872-125B9
|fonse_treatment=EFO:0000369,FF:0000625,FF:0000631,FF:0011444,FF:11872-125B9
|fonse_treatment_closure=EFO:0000369,FF:0000625,FF:0000631,FF:0011444,FF:11872-125B9
|fonse_treatment_closure=EFO:0000369,FF:0000625,FF:0000631,FF:0011444,FF:11872-125B9
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11872-125B9
|is_a=EFO:0002091;;FF:0000002;;FF:0000210;;FF:0011444
|is_a=EFO:0002091;;FF:0000002;;FF:0000210;;FF:0011444
|name=CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor2
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs13483,LSID1025,release012,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=125
|rna_catalog_number=
|rna_concentration=0.61499
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=D4-3
|rna_od260/230=1.47
|rna_od260/280=2.02
|rna_position=B9
|rna_rin=8.6
|rna_sample_type=total RNA
|rna_tube_id=125B9
|rna_weight_ug=2.767455
|sample_age=51
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=monocyte
|sample_collaboration=Christine Wells (University of Queensland)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=donor2
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11872
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=
|top_motifs=STAT5{A,B}:5.12668448578;STAT2,4,6:5.03089260174;FOSL2:4.35330268841;NFE2:4.13587006393;NFE2L2:3.97044467941;IRF7:3.88216735301;BACH2:3.79385448957;FOS_FOS{B,L1}_JUN{B,D}:3.68954908866;CEBPA,B_DDIT3:3.65082218866;STAT1,3:3.63491530742;IRF1,2:3.48788532449;PAX2:3.29444876047;SREBF1,2:3.23344360894;FOXP3:2.8994923943;SPIB:2.83128537095;HLF:2.82119223775;EP300:2.68986224218;SPI1:2.58160095642;NFE2L1:2.52860649275;ATF4:2.45463286651;ATF5_CREB3:2.45165759864;ETS1,2:2.36346500426;DMAP1_NCOR{1,2}_SMARC:2.33660139343;ZBTB16:2.26837197234;ATF6:2.22837056231;NR1H4:2.12577640531;NANOG{mouse}:2.08186889786;NFIL3:2.06869016154;FOXN1:2.06861133661;NFKB1_REL_RELA:1.79006153193;CREB1:1.76535031658;RUNX1..3:1.74508394576;HSF1,2:1.47855772079;TGIF1:1.40856811394;MAFB:1.29031364784;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.2606442459;BPTF:1.24505782279;JUN:1.21831284565;ELF1,2,4:1.15230445072;FOXD3:1.13912146131;ALX4:1.12218186949;PDX1:1.12031323798;PITX1..3:1.11107397678;CDX1,2,4:1.07765365543;PAX8:1.07160746652;ATF2:0.9910452418;PAX3,7:0.847075602315;HIF1A:0.835466443252;NFATC1..3:0.821466804411;PAX4:0.797434560957;HMGA1,2:0.777929458913;TLX2:0.677333480341;FOXP1:0.651101752959;ESRRA:0.579693231845;HBP1_HMGB_SSRP1_UBTF:0.57091417527;IKZF2:0.506790634257;NKX6-1,2:0.458215435238;SRF:0.421289881899;HMX1:0.419651337906;NR6A1:0.398340617483;GLI1..3:0.351891202323;XBP1:0.280600748722;GATA4:0.261480362833;SMAD1..7,9:0.243715164772;RFX2..5_RFXANK_RFXAP:0.188497340558;AHR_ARNT_ARNT2:0.159298558501;HOX{A6,A7,B6,B7}:0.112234129361;HES1:0.105491649113;PRDM1:0.0822452255267;PPARG:0.0633856732171;FOXM1:0.0500906322778;ESR1:0.0331181296572;NANOG:0.00153848505765;FOXO1,3,4:-0.0134042499449;HOX{A5,B5}:-0.0898213355183;OCT4_SOX2{dimer}:-0.163367040004;FOX{D1,D2}:-0.173285623469;RXRA_VDR{dimer}:-0.183523824702;TBP:-0.184560764647;TFCP2:-0.189284414088;FOXL1:-0.203166070783;NKX3-1:-0.248654715694;EN1,2:-0.253523965796;MYB:-0.257064720997;NKX3-2:-0.276373976464;RREB1:-0.296802932587;EGR1..3:-0.306828697872;ALX1:-0.340712723433;MEF2{A,B,C,D}:-0.425192470982;RBPJ:-0.449585812445;POU1F1:-0.487722152729;POU2F1..3:-0.557511552512;HOXA9_MEIS1:-0.566312264761;RXR{A,B,G}:-0.691360253237;POU5F1:-0.698324874337;MZF1:-0.703405132348;FOX{F1,F2,J1}:-0.712361755655;TFAP4:-0.732205739743;SPZ1:-0.76546576034;TOPORS:-0.799738241691;PAX1,9:-0.833390718504;T:-0.84904816571;REST:-0.857118518586;AIRE:-0.868855166708;HNF4A_NR2F1,2:-0.871183699088;IKZF1:-0.873003064988;DBP:-0.897578840758;VSX1,2:-0.906223033922;ZNF384:-0.945011471813;MYFfamily:-1.00273752237;POU6F1:-1.01709568311;GZF1:-1.02786299085;SOX2:-1.04924576787;NHLH1,2:-1.09736491452;MED-1{core}:-1.10108705858;NKX2-2,8:-1.12302078828;PAX6:-1.13852625057;HNF1A:-1.15137503476;PRRX1,2:-1.17059312582;ZNF238:-1.17962305522;CUX2:-1.19127184369;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.2286112904;GATA6:-1.24913383098;TEF:-1.25211526109;MYBL2:-1.31867271189;RORA:-1.336407544;MTE{core}:-1.34399193791;TFAP2B:-1.38433734524;NKX2-3_NKX2-5:-1.40420945834;ZBTB6:-1.41058005389;ZFP161:-1.46063890475;PATZ1:-1.48942899278;UFEwm:-1.50612572237;NKX2-1,4:-1.51180519922;TAL1_TCF{3,4,12}:-1.5213021723;EVI1:-1.528880108;MTF1:-1.53159483942;ZEB1:-1.56479077072;BREu{core}:-1.57289241142;GCM1,2:-1.57705868003;TEAD1:-1.57805002556;RFX1:-1.59136458035;MYOD1:-1.61796159247;XCPE1{core}:-1.64007440977;SP1:-1.64273274375;TFAP2{A,C}:-1.6614132917;ADNP_IRX_SIX_ZHX:-1.70956599049;GTF2A1,2:-1.71468151743;NR3C1:-1.71480015695;SOX5:-1.73416802447;MAZ:-1.74766102475;FOXA2:-1.75510185931;TP53:-1.77576688739;E2F1..5:-1.78407463462;SOX{8,9,10}:-1.7904142238;TLX1..3_NFIC{dimer}:-1.83192928968;KLF4:-1.8381477702;GTF2I:-1.8493496706;SNAI1..3:-1.91775042518;ZIC1..3:-1.97403977245;ZNF148:-1.98160710731;HOX{A4,D4}:-1.98738921054;TFDP1:-1.99803967906;ONECUT1,2:-2.04279279928;HAND1,2:-2.05974530821;bHLH_family:-2.08396051588;HIC1:-2.09975967271;GFI1B:-2.14037461048;CRX:-2.17578353558;LMO2:-2.20902119273;EBF1:-2.21032297014;NFY{A,B,C}:-2.28284406139;TBX4,5:-2.29700576208;ELK1,4_GABP{A,B1}:-2.31832110651;POU3F1..4:-2.33147520338;NFIX:-2.33606849779;FOX{I1,J2}:-2.3406598515;ZNF423:-2.4442591629;PBX1:-2.50949805721;CDC5L:-2.52386838421;SOX17:-2.56505132643;FOXQ1:-2.59948962023;NR5A1,2:-2.71595325871;NRF1:-2.87442802939;GFI1:-2.93728341334;YY1:-2.97542797272;AR:-3.06800352126;PAX5:-3.13341234337;ARID5B:-3.25121076633;LHX3,4:-3.39587309478;ZNF143:-3.5859174552;LEF1_TCF7_TCF7L1,2:-3.69292127005
}}
}}

Revision as of 15:04, 21 March 2012


Name:CD14+ monocytes - treated with Trehalose dimycolate (TDM), donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
age51
cell typemonocyte
cell lineNA
companyNA
collaborationChristine Wells (University of Queensland)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberD4-3
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-Peripheral0.489
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-penis0.0798
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0.755
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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-Whole0.182
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: CNhs13483

Jaspar motifP-value
MA0002.23.87615e-5
MA0003.10.78
MA0004.10.232
MA0006.10.626
MA0007.10.7
MA0009.10.128
MA0014.10.958
MA0017.10.0744
MA0018.20.141
MA0019.10.41
MA0024.10.00173
MA0025.10.0611
MA0027.10.773
MA0028.10.0692
MA0029.10.129
MA0030.10.0744
MA0031.10.251
MA0035.20.129
MA0038.10.0895
MA0039.20.592
MA0040.10.755
MA0041.10.125
MA0042.10.191
MA0043.11.77989e-5
MA0046.10.014
MA0047.20.678
MA0048.10.659
MA0050.13.12574e-18
MA0051.12.6217e-10
MA0052.10.151
MA0055.10.871
MA0057.10.585
MA0058.10.0827
MA0059.10.135
MA0060.11.37103e-9
MA0061.11.94552e-6
MA0062.20.91
MA0065.20.0172
MA0066.10.0504
MA0067.13.32874e-6
MA0068.10.12
MA0069.10.699
MA0070.10.023
MA0071.10.41
MA0072.10.993
MA0073.10.59
MA0074.10.192
MA0076.10.0692
MA0077.10.158
MA0078.10.554
MA0079.20.207
MA0080.26.91083e-13
MA0081.16.77685e-4
MA0083.10.604
MA0084.10.639
MA0087.10.571
MA0088.10.559
MA0090.10.335
MA0091.10.547
MA0092.10.335
MA0093.10.277
MA0099.26.84828e-42
MA0100.10.734
MA0101.14.3414e-5
MA0102.22.30064e-6
MA0103.10.278
MA0104.20.327
MA0105.13.36054e-11
MA0106.10.871
MA0107.16.87442e-6
MA0108.20.0751
MA0111.10.565
MA0112.24.67695e-5
MA0113.10.754
MA0114.10.197
MA0115.10.789
MA0116.15.39579e-4
MA0117.10.0917
MA0119.10.178
MA0122.10.971
MA0124.10.622
MA0125.10.34
MA0131.10.417
MA0135.10.43
MA0136.12.54322e-12
MA0137.27.6169e-10
MA0138.20.446
MA0139.10.715
MA0140.10.204
MA0141.10.165
MA0142.10.735
MA0143.10.955
MA0144.11.46789e-4
MA0145.10.45
MA0146.10.19
MA0147.10.404
MA0148.10.748
MA0149.10.197
MA0150.15.50376e-20
MA0152.10.753
MA0153.10.00511
MA0154.10.00178
MA0155.10.949
MA0156.15.08575e-7
MA0157.10.975
MA0159.10.0321
MA0160.10.0445
MA0162.10.68
MA0163.12.37525e-8
MA0164.10.534
MA0258.10.00311
MA0259.10.947



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: CNhs13483

Novel motifP-value
10.0749
100.018
1000.916
1010.836
1020.767
1030.378
1040.609
1050.217
1066.8682e-4
1070.211
1080.94
1090.303
110.156
1100.134
1110.023
1120.322
1130.43
1140.0118
1150.306
1160.844
1170.0644
1180.166
1190.118
120.376
1200.708
1210.468
1220.801
1230.0351
1240.749
1250.369
1260.343
1270.436
1280.032
1290.537
130.106
1300.0767
1310.573
1320.0685
1330.648
1340.612
1350.81
1360.602
1370.0149
1380.153
1390.0309
140.433
1400.168
1410.288
1420.0968
1430.0477
1440.682
1450.285
1460.577
1470.503
1480.00931
1490.939
150.169
1500.433
1510.361
1520.232
1530.778
1540.319
1550.732
1560.484
1570.395
1580.0118
1590.667
160.353
1600.301
1610.403
1620.299
1630.121
1640.0747
1650.147
1660.702
1670.083
1680.381
1690.00817
170.211
180.177
190.383
20.642
200.247
210.421
220.333
230.0444
240.345
250.394
260.0566
270.676
280.516
290.233
30.0959
300.439
310.849
320.813
330.316
340.71
350.17
360.0742
370.0775
380.388
390.844
40.944
400.251
410.0257
420.372
430.0429
440.993
450.929
460.151
470.502
480.462
490.123
50.276
500.931
510.445
520.394
530.39
540.368
550.41
560.701
570.665
580.122
590.35
60.711
600.0488
610.621
620.0637
630.5
640.411
650.23
660.224
670.576
680.927
690.578
70.278
700.0251
710.0377
720.211
730.203
740.15
750.124
760.174
770.596
780.108
790.296
80.39
800.493
810.302
820.205
830.0759
840.364
850.0195
860.0568
870.728
880.659
890.368
90.514
900.0745
910.221
920.211
930.502
940.0557
950.513
960.46
970.771
980.104
990.0594



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: CNhs13483


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)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic 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)
0000860 (classical monocyte)
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)
0002057 (CD14-positive, CD16-negative classical monocyte)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
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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