Supplementary Table 1 Primer sequences
Gene / Fw sequences 5' to 3' / Rv sequence 5' to 3' / ProbeDAZL / CTCCGGCTTATTCAGCTGT / ATTGCCCGACTTCTTCTAAAG
DDR1 / GGCCACACTCAACTTTGTACATC / AAAGGCCCACACGTCACTC
XIST / TCAGGAGGTTCTGTCAAGAT / AAATGGGTAAGACACATTTAGA
ACRC / CTGCCAGAGAAACTACGC / AGGATACACCCGGAGCT
RASSF1A / TCTGGGGAGGTGAACTG / ACTGGCCCTGTCACACT / FAM-TATTGCCGCCAGAATATCCA-TAMRA
Supplementary Table 2. Methylation differences between groups of neuro-ectodermal cell lines
2a. Most significant methylation probes discriminating NBL and PNET (top50 Limma)
Positive logFC means higher level of methylation in NBL versus PNETs, negative log FC means higher methylation levels in PNETs than NBL.
ProbeName / GeneName / Chromosomal location / Position / 2logFC / P.Value / adj.P.ValA_17_P02907066 / chr4:006165350-006165395 / chr4:006165350-006165395 / Unknown / -2.01 / 1.02E-09 / 1.61E-04
A_17_P08361959 / HOXC13 / chr12:052625251-052625295 / INSIDE / 1.58 / 1.32E-09 / 1.61E-04
A_17_P04550267 / TFAP2A / chr6:010525832-010525884 / PROMOTER / 2.68 / 2.17E-09 / 1.76E-04
A_17_P11444345 / DERL3 / chr22:022511447-022511491 / PROMOTER / -3.31 / 3.30E-09 / 2.01E-04
A_17_P04550287 / TFAP2A / chr6:010530396-010530440 / PROMOTER / 1.51 / 1.77E-08 / 7.63E-04
A_17_P15784737 / TFAP2A / chr6:010525875-010525919 / PROMOTER / 1.78 / 1.88E-08 / 7.63E-04
A_17_P10350247 / HOXB5 / chr17:044025873-044025917 / INSIDE / 2.55 / 3.44E-08 / 1.20E-03
A_17_P07786694 / ALX4 / chr11:044282931-044282980 / INSIDE / 1.33 / 4.70E-08 / 1.27E-03
A_17_P11265916 / KCNQ2 / chr20:061567552-061567596 / INSIDE / -1.15 / 4.67E-08 / 1.27E-03
A_17_P10975351 / EML2 / chr19:050836672-050836720 / PROMOTER / -2.33 / 6.18E-08 / 1.37E-03
A_17_P07246577 / chr10:059536509-059536555 / chr10:059536509-059536555 / Unknown / -1.57 / 5.80E-08 / 1.37E-03
A_17_P05915663 / MYOM2 / chr8:002025200-002025246 / INSIDE / 2.24 / 9.36E-08 / 1.57E-03
A_17_P01473075 / chr2:128967364-128967409 / chr2:128967364-128967409 / Unknown / -1.90 / 8.06E-08 / 1.57E-03
A_17_P00567792 / LMX1A / chr1:163588930-163588980 / INSIDE / 2.70 / 9.66E-08 / 1.57E-03
A_17_P00489894 / TBX15 / chr1:119333660-119333704 / INSIDE / 1.71 / 9.31E-08 / 1.57E-03
A_17_P05884267 / DPP6 / chr7:154216703-154216747 / INSIDE / -1.75 / 1.15E-07 / 1.65E-03
A_17_P11444347 / DERL3 / chr22:022511615-022511659 / PROMOTER / -1.64 / 1.13E-07 / 1.65E-03
A_17_P04549988 / chr6:010492121-010492177 / chr6:010492121-010492177 / Unknown / 1.70 / 1.27E-07 / 1.72E-03
A_17_P07395392 / chr10:094170798-094170844 / chr10:094170798-094170844 / Unknown / -1.47 / 1.39E-07 / 1.78E-03
A_17_P04550286 / TFAP2A / chr6:010530215-010530259 / PROMOTER / 1.27 / 1.56E-07 / 1.86E-03
A_17_P07395391 / chr10:094170738-094170788 / chr10:094170738-094170788 / Unknown / -1.66 / 1.61E-07 / 1.86E-03
A_17_P00529213 / BCAN / chr1:154883552-154883596 / INSIDE / -1.59 / 1.94E-07 / 1.92E-03
A_17_P00914926 / ZNF238 / chr1:242280244-242280303 / PROMOTER / 0.98 / 2.05E-07 / 1.92E-03
A_17_P04549999 / chr6:010493250-010493304 / chr6:010493250-010493304 / Unknown / 1.57 / 2.05E-07 / 1.92E-03
A_17_P00567790 / LMX1A / chr1:163588780-163588824 / INSIDE / 1.42 / 1.99E-07 / 1.92E-03
A_17_P11052979 / C20orf103 / chr20:009435271-009435315 / PROMOTER / -1.25 / 1.78E-07 / 1.92E-03
A_17_P07681914 / SLC6A5 / chr11:020575549-020575594 / PROMOTER / -2.18 / 2.27E-07 / 2.04E-03
A_17_P05915661 / MYOM2 / chr8:002025051-002025110 / INSIDE / 1.59 / 2.37E-07 / 2.06E-03
A_17_P04940168 / GRIK2 / chr6:101953676-101953721 / INSIDE / 2.19 / 3.63E-07 / 2.82E-03
A_17_P11052980 / C20orf103 / chr20:009435475-009435534 / PROMOTER / -1.38 / 3.77E-07 / 2.82E-03
A_17_P02631057 / GRK7 / chr3:142999033-142999085 / INSIDE / -1.47 / 3.56E-07 / 2.82E-03
A_17_P08362120 / HOXC11 / chr12:052646071-052646127 / PROMOTER / 1.23 / 3.82E-07 / 2.82E-03
A_17_P11444346 / DERL3 / chr22:022511521-022511565 / PROMOTER / -1.63 / 3.59E-07 / 2.82E-03
A_17_P05915662 / MYOM2 / chr8:002025136-002025180 / INSIDE / 1.92 / 4.87E-07 / 3.12E-03
A_17_P02000215 / chr2:240527138-240527182 / chr2:240527138-240527182 / Unknown / -0.96 / 4.42E-07 / 3.12E-03
A_17_P10350244 / HOXB5 / chr17:044025453-044025506 / INSIDE / 1.70 / 4.69E-07 / 3.12E-03
A_17_P05915664 / MYOM2 / chr8:002025300-002025346 / INSIDE / 2.38 / 4.52E-07 / 3.12E-03
A_17_P11550465 / SBF1 / chr22:049245254-049245298 / INSIDE / 2.44 / 4.78E-07 / 3.12E-03
A_17_P15784658 / chr6:010490212-010490256 / chr6:010490212-010490256 / Unknown / 0.93 / 5.25E-07 / 3.18E-03
A_17_P11444340 / DERL3 / chr22:022510605-022510649 / INSIDE / -2.44 / 5.15E-07 / 3.18E-03
A_17_P08362119 / HOXC11 / chr12:052645983-052646032 / PROMOTER / 2.21 / 5.35E-07 / 3.18E-03
A_17_P04940167 / GRIK2 / chr6:101953514-101953560 / PROMOTER / 2.61 / 5.60E-07 / 3.24E-03
A_17_P01064707 / ZNF512 / chr2:027659630-027659677 / INSIDE / -1.64 / 5.84E-07 / 3.31E-03
A_17_P10350237 / HOXB5 / chr17:044024590-044024642 / INSIDE / 1.48 / 6.01E-07 / 3.33E-03
A_17_P10350249 / HOXB5 / chr17:044026017-044026069 / INSIDE / 1.84 / 7.06E-07 / 3.82E-03
A_17_P10350449 / HOXB8 / chr17:044052345-044052398 / PROMOTER / 1.85 / 7.59E-07 / 3.93E-03
A_17_P01135357 / chr2:043181864-043181910 / chr2:043181864-043181910 / Unknown / -1.46 / 7.46E-07 / 3.93E-03
A_17_P07362142 / LRRC21 / chr10:085987412-085987457 / INSIDE / -1.42 / 8.26E-07 / 4.19E-03
A_17_P16440110 / ALX4 / chr11:044281484-044281528 / INSIDE / 2.02 / 9.39E-07 / 4.61E-03
A_17_P03629274 / HAND2 / chr4:174676434-174676478 / DOWNSTREAM / 1.49 / 9.48E-07 / 4.61E-03
2b. Most significant methylation probes discriminating two NBL clusters (n=46)
ProbeName / GeneName / SystematicName / Description / 2logFC / P.Value / adj.P.ValA_17_P08176318 / HOM-TES-103 / chr12:006527932-006527977 / INSIDE / 1.91 / 4.93E-09 / 1.20E-03
A_17_P16363912 / ANXA11 / chr10:081957305-081957349 / PROMOTER / 1.80 / 3.21E-08 / 3.04E-03
A_17_P16915418 / chr16:075803989-075804033 / chr16:075803989-075804033 / Unknown / 1.31 / 3.74E-08 / 3.04E-03
A_17_P15210253 / MYT1L / chr2:002169069-002169113 / INSIDE / 1.20 / 1.05E-07 / 6.38E-03
A_17_P04300424 / chr5:134855293-134855344 / chr5:134855293-134855344 / Unknown / -1.78 / 1.90E-07 / 8.40E-03
LACC:SRN_31200 / LACC:SRN_31200 / LACC:SRN_31200 / 1.41 / 2.08E-07 / 8.40E-03
A_17_P05912740 / DLGAP2 / chr8:001482469-001482513 / INSIDE / 1.34 / 2.41E-07 / 8.40E-03
A_17_P03711303 / TRIP13 / chr5:000965465-000965510 / INSIDE / 1.51 / 3.76E-07 / 1.15E-02
A_17_P09783417 / ARNT2 / chr15:078483047-078483097 / PROMOTER / -1.17 / 4.51E-07 / 1.22E-02
A_17_P09150169 / FLJ41484 / chr13:113567401-113567445 / INSIDE / 1.40 / 5.93E-07 / 1.22E-02
LACC:SRN_30551 / LACC:SRN_30551 / LACC:SRN_30551 / 1.26 / 5.93E-07 / 1.22E-02
A_17_P00940553 / TPO / chr2:001523176-001523235 / INSIDE / 1.62 / 6.02E-07 / 1.22E-02
A_17_P09395147 / FOS / chr14:074816572-074816616 / INSIDE / -1.66 / 1.04E-06 / 1.58E-02
A_17_P03711304 / TRIP13 / chr5:000965542-000965586 / INSIDE / 1.85 / 9.64E-07 / 1.58E-02
A_17_P15172339 / chr1:211629644-211629696 / chr1:211629644-211629696 / Unknown / 1.82 / 1.01E-06 / 1.58E-02
A_17_P05257584 / DLL1 / chr6:170439370-170439414 / INSIDE / 1.98 / 1.01E-06 / 1.58E-02
A_17_P05249844 / SMOC2 / chr6:168699292-168699336 / INSIDE / 1.46 / 1.17E-06 / 1.67E-02
A_17_P07548634 / CTBP2 / chr10:126702248-126702304 / INSIDE / -1.48 / 1.32E-06 / 1.78E-02
A_17_P07600674 / MRPL23 / chr11:001934867-001934911 / DOWNSTREAM / -1.45 / 1.60E-06 / 2.05E-02
A_17_P02574909 / GATA2 / chr3:129693194-129693241 / INSIDE / -1.37 / 1.78E-06 / 2.07E-02
A_17_P11198300 / chr20:046435094-046435139 / chr20:046435094-046435139 / Unknown / 1.23 / 1.76E-06 / 2.07E-02
A_17_P01391086 / chr2:107527205-107527249 / chr2:107527205-107527249 / Unknown / 1.50 / 2.01E-06 / 2.13E-02
A_17_P10976047 / SYMPK-FOXA3 / chr19:051059144-051059188 / DIVERGENT_
PROMOTER / 0.83 / 1.97E-06 / 2.13E-02
A_17_P05912414 / DLGAP2 / chr8:001429032-001429076 / PROMOTER / 0.88 / 2.44E-06 / 2.32E-02
A_17_P05248699 / chr6:168508598-168508642 / chr6:168508598-168508642 / Unknown / 1.32 / 2.48E-06 / 2.32E-02
A_17_P02574911 / GATA2 / chr3:129693434-129693486 / INSIDE / -1.72 / 2.48E-06 / 2.32E-02
A_17_P09150170 / FLJ41484 / chr13:113567653-113567697 / INSIDE / 1.50 / 3.03E-06 / 2.63E-02
A_17_P10545239 / APCDD1 / chr18:010461875-010461919 / INSIDE / 1.27 / 2.93E-06 / 2.63E-02
A_17_P10955511 / SIPA1L3 / chr19:043392247-043392291 / DOWNSTREAM / -1.26 / 3.25E-06 / 2.73E-02
A_17_P05288557 / NXPH1 / chr7:008449923-008449967 / INSIDE / 2.32 / 4.22E-06 / 3.29E-02
A_17_P10035350 / MT1E / chr16:055217161-055217209 / INSIDE / -1.31 / 4.20E-06 / 3.29E-02
A_17_P05257465 / chr6:170422894-170422938 / chr6:170422894-170422938 / Unknown / 1.86 / 4.33E-06 / 3.29E-02
A_17_P02574910 / GATA2 / chr3:129693284-129693328 / INSIDE / -1.41 / 4.64E-06 / 3.42E-02
A_17_P06011560 / chr8:023616576-023616624 / chr8:023616576-023616624 / Unknown / -1.03 / 5.19E-06 / 3.72E-02
A_17_P10220321 / chr17:008848299-008848352 / chr17:008848299-008848352 / Unknown / -1.21 / 5.56E-06 / 3.76E-02
A_17_P16279975 / FLJ20433 / chr9:139388610-139388654 / INSIDE / 0.89 / 5.54E-06 / 3.76E-02
A_17_P07600668 / MRPL23 / chr11:001934065-001934109 / INSIDE / -1.51 / 5.75E-06 / 3.79E-02
A_17_P15395483 / SH3BP4 / chr2:235525080-235525124 / PROMOTER / 0.75 / 5.94E-06 / 3.81E-02
A_17_P06345416 / chr8:103820157-103820201 / chr8:103820157-103820201 / Unknown / 2.06 / 6.23E-06 / 3.89E-02
A_17_P10088936 / SMPD3 / chr16:066963546-066963590 / INSIDE / 1.43 / 6.56E-06 / 3.99E-02
A_17_P04818296 / chr6:074076075-074076134 / chr6:074076075-074076134 / Unknown / 1.86 / 6.78E-06 / 4.03E-02
A_17_P15653240 / CEP72 / chr5:000676366-000676410 / INSIDE / -0.89 / 7.05E-06 / 4.09E-02
A_17_P10955512 / SIPA1L3 / chr19:043392468-043392514 / DOWNSTREAM / -1.57 / 8.53E-06 / 4.79E-02
A_17_P09472923 / SMEK1 / chr14:091045592-091045636 / INSIDE / 0.90 / 8.65E-06 / 4.79E-02
A_17_P17085040 / chr18:072191534-072191578 / chr18:072191534-072191578 / Unknown / 0.90 / 9.17E-06 / 4.96E-02
Supplementary Table 3: Demethylating treatment effects of DAC and TSA in NBL and PNET cell lines
Supplementary Table 3a
CpG island probes demethylating >1.5 FC in all NBL cell lines (adj. P-value<0.05). Last colum shows number of cell lines that showed a demethylating effect of at least 1.5 fold (Limma).
ProbeName / GeneName / SystematicName / Description / logFC / FC demethylation / adj.P.Val / No of cell linesA_17_P10894655 / ABHD9 / chr19:015205042-015205086 / PROMOTER / -0.79 / 1.73 / 0.000116 / 10
A_17_P05593063 / ADAM22 / chr7:087401243-087401287 / PROMOTER / -0.59 / 1.50 / 0.005493 / 8
A_17_P00948985 / ALLC / chr2:003677230-003677274 / PROMOTER / -0.61 / 1.53 / 0.002942 / 5
A_17_P16619811 / ATP8A2 / chr13:024844145-024844189 / PROMOTER / -0.62 / 1.54 / 0.000592 / 9
A_17_P00120325 / BAI2 / chr1:032010777-032010821 / PROMOTER / -0.62 / 1.54 / 0.001024 / 8
A_17_P10491259 / BAIAP2 / chr17:076621379-076621423 / PROMOTER / -0.81 / 1.76 / 0.000169 / 13
A_17_P10491260 / BAIAP2 / chr17:076621494-076621538 / PROMOTER / -0.69 / 1.61 / 0.000221 / 9
A_17_P10491257 / BAIAP2 / chr17:076621133-076621177 / PROMOTER / -0.67 / 1.59 / 0.000323 / 9
A_17_P10491258 / BAIAP2 / chr17:076621232-076621277 / PROMOTER / -0.65 / 1.56 / 0.000145 / 10
A_17_P17273625 / C22orf31-KREMEN1 / chr22:027797214-027797261 / DIVERGENT_PROMOTER / -0.63 / 1.55 / 0.000489 / 7
A_17_P15384207 / C2orf24-C2orf17 / chr2:219750046-219750090 / DIVERGENT_PROMOTER / -0.67 / 1.60 / 0.002191 / 10
A_17_P01330136 / CAPG / chr2:085494826-085494883 / PROMOTER / -0.60 / 1.51 / 0.000411 / 8
A_17_P17022879 / CBX8 / chr17:075389606-075389650 / PROMOTER / -0.65 / 1.57 / 0.000076 / 7
A_17_P17022880 / CBX8 / chr17:075389684-075389728 / PROMOTER / -0.62 / 1.54 / 0.000177 / 9
A_17_P07833726 / CHRM1 / chr11:062450280-062450324 / PROMOTER / -0.81 / 1.75 / 0.000025 / 11
A_17_P07833731 / CHRM1 / chr11:062451086-062451130 / PROMOTER / -0.78 / 1.72 / 0.000137 / 9
A_17_P07796427 / CHRM4 / chr11:046368712-046368756 / PROMOTER / -0.67 / 1.60 / 0.000200 / 8
A_17_P09792521 / CPEB1 / chr15:081114480-081114524 / PROMOTER / -0.63 / 1.55 / 0.000151 / 9
A_17_P16908074 / CTF8-CIRH1A / chr16:067723984-067724028 / DIVERGENT_PROMOTER / -0.70 / 1.62 / 0.001495 / 8
A_17_P04650749 / DAXX / chr6:033399033-033399077 / PROMOTER / -0.62 / 1.54 / 0.000180 / 6
A_17_P01675412 / DLX1 / chr2:172654359-172654403 / PROMOTER / -0.64 / 1.56 / 0.000076 / 8
A_17_P05635574 / DLX6 / chr7:096469776-096469827 / PROMOTER / -0.59 / 1.51 / 0.000279 / 8
A_17_P07435547 / FGF8 / chr10:103528850-103528894 / PROMOTER / -0.64 / 1.56 / 0.000144 / 9
A_17_P10262023 / FLJ31196 / chr17:019568922-019568981 / PROMOTER / -0.59 / 1.51 / 0.000025 / 7
A_17_P10477068 / FLJ45079 / chr17:073395616-073395668 / PROMOTER / -0.65 / 1.57 / 0.000164 / 9
A_17_P10477072 / FLJ45079 / chr17:073395968-073396025 / PROMOTER / -0.61 / 1.52 / 0.001329 / 7
A_17_P10497698 / FN3K / chr17:078280617-078280665 / PROMOTER / -0.65 / 1.57 / 0.000103 / 8
A_17_P11498831 / GALR3 / chr22:036544934-036544978 / PROMOTER / -0.62 / 1.54 / 0.000122 / 9
A_17_P01902071 / GMPPA / chr2:220069908-220069952 / PROMOTER / -0.69 / 1.61 / 0.001080 / 10
A_17_P06339525 / GRHL2 / chr8:102574038-102574082 / PROMOTER / -0.69 / 1.62 / 0.000536 / 9
A_17_P08362681 / HOXC5 / chr12:052711417-052711463 / PROMOTER / -0.61 / 1.52 / 0.000256 / 6
A_17_P08362481 / HOXC8 / chr12:052686755-052686799 / PROMOTER / -0.62 / 1.54 / 0.000988 / 9
A_17_P15751795 / hsa-mir-378 / chr5:149090318-149090362 / PROMOTER / -0.62 / 1.54 / 0.000482 / 9
A_17_P05914004 / hsa-mir-596 / chr8:001752238-001752282 / PROMOTER / -0.79 / 1.72 / 0.000025 / 9
A_17_P05914005 / hsa-mir-596 / chr8:001752498-001752543 / PROMOTER / -0.63 / 1.55 / 0.000083 / 7
A_17_P07046049 / IL15RA / chr10:006059826-006059870 / PROMOTER / -0.70 / 1.63 / 0.000751 / 11
A_17_P10323171 / KRT19 / chr17:036938161-036938207 / PROMOTER / -0.67 / 1.60 / 0.000309 / 6
A_17_P01281693 / LBX2 / chr2:074584452-074584500 / PROMOTER / -0.69 / 1.62 / 0.000061 / 9
A_17_P00299436 / LHX8 / chr1:075363867-075363921 / PROMOTER / -0.70 / 1.62 / 0.000101 / 10
A_17_P10989818 / LOC554235 / chr19:055712219-055712264 / PROMOTER / -0.64 / 1.56 / 0.000082 / 10
A_17_P17100023 / MAP2K2 / chr19:004075142-004075186 / PROMOTER / -0.61 / 1.53 / 0.000343 / 7
A_17_P16844319 / MGC52282 / chr16:002832793-002832837 / PROMOTER / -0.60 / 1.52 / 0.000280 / 6
A_17_P04828257 / MYO6 / chr6:076515092-076515136 / PROMOTER / -0.65 / 1.57 / 0.000772 / 8
A_17_P16280246 / NELF / chr9:139473671-139473715 / PROMOTER / -0.61 / 1.52 / 0.000954 / 8
A_17_P16374403 / PDLIM1 / chr10:097045147-097045191 / PROMOTER / -0.59 / 1.50 / 0.001090 / 8
A_17_P02178511 / PLCD1-DLEC1 / chr3:038046584-038046630 / DIVERGENT_PROMOTER / -0.65 / 1.57 / 0.010029 / 8
A_17_P16986419 / PLCD3-ACBD4 / chr17:040565754-040565798 / DIVERGENT_PROMOTER / -0.65 / 1.57 / 0.000305 / 7
A_17_P08706302 / PSPC1 / chr13:019255270-019255329 / PROMOTER / -0.60 / 1.52 / 0.000237 / 6
A_17_P08344503 / RACGAP1 / chr12:048713040-048713084 / PROMOTER / -0.72 / 1.65 / 0.000115 / 11
A_17_P11234328 / RBM38 / chr20:055398602-055398646 / PROMOTER / -0.67 / 1.60 / 0.000072 / 10
A_17_P11234327 / RBM38 / chr20:055398314-055398358 / PROMOTER / -0.66 / 1.58 / 0.000061 / 8
A_17_P11234332 / RBM38 / chr20:055399277-055399323 / PROMOTER / -0.60 / 1.52 / 0.000180 / 8
A_17_P01360964 / RPL31 / chr2:100984842-100984890 / PROMOTER / -0.62 / 1.53 / 0.000796 / 8
A_17_P10959299 / RPS16-SUPT5H / chr19:044618707-044618764 / DIVERGENT_PROMOTER / -0.66 / 1.58 / 0.001002 / 9
A_17_P00516449 / S100A6 / chr1:151775329-151775373 / PROMOTER / -0.63 / 1.54 / 0.000136 / 6
A_17_P07346732 / SH2D4B / chr10:082285985-082286029 / PROMOTER / -0.64 / 1.55 / 0.000083 / 7
A_17_P15369680 / SLC39A10 / chr2:196230013-196230057 / PROMOTER / -0.61 / 1.53 / 0.000187 / 9
A_17_P10404639 / TBX2 / chr17:056828248-056828292 / PROMOTER / -0.70 / 1.62 / 0.000259 / 9
A_17_P10404635 / TBX2 / chr17:056827913-056827957 / PROMOTER / -0.62 / 1.54 / 0.000620 / 10
A_17_P10404877 / TBX4 / chr17:056886544-056886588 / PROMOTER / -0.80 / 1.75 / 0.000019 / 11
A_17_P10404881 / TBX4 / chr17:056887479-056887523 / PROMOTER / -0.80 / 1.74 / 0.000042 / 10
A_17_P10404876 / TBX4 / chr17:056886454-056886500 / PROMOTER / -0.63 / 1.55 / 0.000043 / 8
A_17_P17003170 / TBX4 / chr17:056886872-056886916 / PROMOTER / -0.59 / 1.51 / 0.000038 / 9
A_17_P00175410 / TESK2-MMACHC / chr1:045738427-045738472 / DIVERGENT_PROMOTER / -0.71 / 1.64 / 0.000845 / 9
A_17_P10275164 / TIAF1 / chr17:024430812-024430856 / PROMOTER / -0.67 / 1.59 / 0.000112 / 9
A_17_P10460886 / TTYH2 / chr17:069720052-069720096 / PROMOTER / -0.64 / 1.56 / 0.000096 / 9
A_17_P10460885 / TTYH2 / chr17:069719992-069720036 / PROMOTER / -0.63 / 1.55 / 0.000257 / 9
A_17_P01281253 / WDR54 / chr2:074496316-074496360 / PROMOTER / -0.63 / 1.55 / 0.000145 / 7
A_17_P01281255 / WDR54 / chr2:074496543-074496587 / PROMOTER / -0.61 / 1.52 / 0.000058 / 9
A_17_P01281254 / WDR54 / chr2:074496438-074496482 / PROMOTER / -0.60 / 1.52 / 0.000150 / 9
A_17_P16598324 / WDR66 / chr12:120840624-120840670 / PROMOTER / -0.61 / 1.53 / 0.002131 / 7
A_17_P08657184 / WDR66 / chr12:120840696-120840740 / PROMOTER / -0.60 / 1.52 / 0.002823 / 9
A_17_P16879057 / ZNF764 / chr16:030480317-030480361 / PROMOTER / -0.62 / 1.54 / 0.000074 / 9
Supplementary Table 3b
Probes demethylating >1.5 FC in all PNET cell lines (adj. P-value<0.05). Last column shows the number of cell lines with a demethylating effect of at least 1.5 fold.
ProbeName / GeneName / SystematicName / Description / logFC / FC demethylation / adj.P.Val / No. of cell linesA_17_P10491259 / BAIAP2 / chr17:076621379-076621423 / PROMOTER / -0.72 / 1.65 / 1.05E-04 / 4
A_17_P10275164 / TIAF1 / chr17:024430812-024430856 / PROMOTER / -0.68 / 1.6 / 2.33E-05 / 3
A_17_P07833731 / CHRM1 / chr11:062451086-062451130 / PROMOTER / -0.66 / 1.58 / 1.80E-04 / 3
A_17_P04828257 / MYO6 / chr6:076515092-076515136 / PROMOTER / -0.64 / 1.56 / 2.84E-04 / 4
A_17_P16908074 / CTF8-CIRH1A / chr16:067723984-067724028 / DIVERGENT_PROMOTER / -0.64 / 1.56 / 7.49E-04 / 2
A_17_P07833726 / CHRM1 / chr11:062450280-062450324 / PROMOTER / -0.61 / 1.52 / 8.80E-05 / 1
A_17_P01281693 / LBX2 / chr2:074584452-074584500 / PROMOTER / -0.61 / 1.52 / 4.97E-05 / 1
A_17_P10404877 / TBX4 / chr17:056886544-056886588 / PROMOTER / -0.61 / 1.52 / 1.69E-05 / 2
A_17_P10497698 / FN3K / chr17:078280617-078280665 / PROMOTER / -0.6 / 1.52 / 9.27E-05 / 2
A_17_P00516449 / S100A6 / chr1:151775329-151775373 / PROMOTER / -0.6 / 1.52 / 8.72E-05 / 2
A_17_P10950208 / POLR2I / chr19:041304146-041304190 / PROMOTER / -0.6 / 1.52 / 3.15E-04 / 3
A_17_P10491260 / BAIAP2 / chr17:076621494-076621538 / PROMOTER / -0.6 / 1.51 / 1.44E-04 / 2
A_17_P17273625 / C22orf31-KREMEN1 / chr22:027797214-027797261 / DIVERGENT_PROMOTER / -0.59 / 1.51 / 4.14E-04 / 1
A_17_P05914004 / hsa-mir-596 / chr8:001752238-001752282 / PROMOTER / -0.59 / 1.51 / 3.81E-05 / 1
A_17_P16321565 / 08-mrt / chr10:045410349-045410393 / PROMOTER / -0.59 / 1.51 / 1.10E-03 / 3
A_17_P10404881 / TBX4 / chr17:056887479-056887523 / PROMOTER / -0.59 / 1.5 / 7.08E-05 / 1
A_17_P00175410 / TESK2-MMACHC / chr1:045738427-045738472 / DIVERGENT_PROMOTER / -0.59 / 1.5 / 1.84E-03 / 2
Supplementary Table 4. Treatment effect of DAC and TSA on gene expression of NBL cell lines
4a. Probes upregulated by DAC and TSA treatment (>1.5 FC, adj. ) in NBL cell lines
Genes that also show significant demethylation of a promoter located methylation probe are boldfaced.
ID / Gene Symbol / Chromosomal Location / logFC / FC / P.Value / adj.P.Val206588_at / DAZL / chr3p24.3 / 3.23 / 25.23 / 3.50E-10 / 3.82E-06
1556395_at / --- / --- / 2.27 / 9.71 / 2.25E-10 / 3.08E-06
231307_at / PAGE2 / chrXp11.21 / 2.18 / 8.84 / 1.00E-10 / 2.74E-06
238825_at / ACRC / chrXq13.1 / 1.77 / 5.90 / 3.98E-09 / 2.22E-05
224588_at / XIST / chrXq13.2 / 1.57 / 4.81 / 1.49E-06 / 5.17E-04
200799_at / HSPA1A / chr6p21.3 / 1.52 / 4.56 / 2.10E-05 / 2.16E-03
206218_at / MAGEB2 / chrXp21.3 / 1.51 / 4.54 / 1.05E-07 / 1.11E-04
201650_at / KRT19 / chr17q21.2 / 1.44 / 4.23 / 9.73E-08 / 1.10E-04
225681_at / CTHRC1 / chr8q22.3 / 1.38 / 3.97 / 1.28E-11 / 7.01E-07
227671_at / XIST / chrXq13.2 / 1.31 / 3.71 / 1.01E-06 / 4.01E-04
214612_x_at / MAGEA6 / chrXq28 / 1.31 / 3.71 / 6.45E-06 / 1.04E-03
214183_s_at / TKTL1 / chrXq28 / 1.23 / 3.43 / 4.08E-04 / 1.41E-02
201631_s_at / IER3 / chr6p21.3 / 1.23 / 3.43 / 1.62E-07 / 1.43E-04
228335_at / CLDN11 / chr3q26.2-q26.3 / 1.19 / 3.29 / 2.25E-05 / 2.25E-03
221577_x_at / GDF15 / chr19p13.1-13.2 / 1.17 / 3.21 / 1.67E-05 / 1.88E-03
202284_s_at / CDKN1A / chr6p21.2 / 1.15 / 3.16 / 5.28E-06 / 9.49E-04
207739_s_at / GAGE1 / GAGE2/ .. / chrXp11.4-p11.2 / chrXp11.23 / 1.12 / 3.06 / 1.62E-06 / 5.32E-04
202016_at / MEST / chr7q32 / 1.11 / 3.02 / 1.02E-06 / 4.03E-04
207281_x_at / VCX / VCX2 /.. / chrXp22 / chrXp22.32 / 1.06 / 2.90 / 7.72E-06 / 1.14E-03
206640_x_at / GAGE2 / GAGE4 /.. / chrXp11.23 / chrXp11.4-p11.2 / 1.04 / 2.82 / 4.05E-06 / 8.37E-04
209942_x_at / MAGEA3 / chrXq28 / 1.03 / 2.79 / 1.35E-05 / 1.64E-03
33323_r_at / SFN / chr1p36.11 / 1.03 / 2.79 / 1.72E-04 / 8.12E-03
221728_x_at / XIST / chrXq13.2 / 0.99 / 2.69 / 4.43E-06 / 8.77E-04
208235_x_at / GAGE7 / chrXp11.4-p11.2 / 0.97 / 2.64 / 8.63E-06 / 1.23E-03
1553599_a_at / SYCP3 / chr12q / 0.97 / 2.63 / 2.26E-07 / 1.80E-04
227801_at / TRIM59 / chr3q26.1 / 0.95 / 2.59 / 4.38E-05 / 3.37E-03
229475_at / MAEL / chr1q24.1 / 0.94 / 2.56 / 3.44E-05 / 2.89E-03
204083_s_at / TPM2 / chr9p13.2-p13.1 / 0.93 / 2.54 / 9.06E-05 / 5.34E-03
214254_at / MAGEA4 / chrXq28 / 0.93 / 2.54 / 1.59E-03 / 3.26E-02
211674_x_at / CTAG1B / CTAG1A /.. / chrXq28 / 0.92 / 2.52 / 7.04E-06 / 1.09E-03
214218_s_at / XIST / chrXq13.2 / 0.92 / 2.52 / 6.55E-06 / 1.05E-03
211403_x_at / VCY /VCX /.. / chrYq11.221 / chrXp22 /.. / 0.92 / 2.51 / 6.43E-06 / 1.04E-03
207086_x_at / GAGE1 / GAGE2 /.. / chrXp11.4-p11.2 / chrXp11.23 / 0.91 / 2.49 / 3.72E-05 / 3.03E-03
210609_s_at / TP53I3 / chr2p23.3 / 0.91 / 2.48 / 2.37E-06 / 6.49E-04
1552368_at / CTCFL / chr20q13.31 / 0.90 / 2.47 / 8.73E-04 / 2.24E-02
223861_at / HORMAD1 / chr1q21.2 / 0.90 / 2.45 / 1.87E-06 / 5.59E-04
208155_x_at / GAGE1 / GAGE4 /.. / chrXp11.4-p11.2 / chrXp11.23 / 0.88 / 2.42 / 1.01E-05 / 1.37E-03
1562209_at / LOC285429 / chr4p13 / 0.87 / 2.38 / 1.88E-06 / 5.59E-04
203186_s_at / S100A4 / chr1q21 / 0.86 / 2.36 / 5.97E-07 / 3.00E-04
225767_at / --- / --- / 0.86 / 2.35 / 1.07E-05 / 1.40E-03
214412_at / H2AFB3 /// H2AFB1 / chrXq28 / 0.85 / 2.35 / 1.85E-05 / 2.01E-03
225912_at / TP53INP1 / chr8q22 / 0.85 / 2.34 / 1.97E-07 / 1.66E-04
202404_s_at / COL1A2 / chr7q22.1 / 0.83 / 2.30 / 1.80E-04 / 8.36E-03
210546_x_at / CTAG1B / CTAG1A /.. / chrXq28 / 0.83 / 2.30 / 3.72E-06 / 7.97E-04
209652_s_at / PGF / chr14q24-q31 / 0.83 / 2.30 / 1.90E-06 / 5.59E-04
39248_at / AQP3 / chr9p13 / 0.83 / 2.28 / 2.92E-06 / 7.12E-04
37796_at / LRCH4 / chr7q22 / 0.82 / 2.28 / 4.69E-07 / 2.57E-04
229331_at / SPATA18 / chr4q12 / 0.82 / 2.27 / 2.96E-05 / 2.65E-03
203607_at / INPP5F / chr10q26.11 / 0.80 / 2.22 / 4.94E-06 / 9.16E-04
224590_at / XIST / chrXq13.2 / 0.79 / 2.21 / 2.88E-06 / 7.09E-04
225573_at / ACAD11 / chr3q22.1 / 0.78 / 2.19 / 2.09E-06 / 5.93E-04
235557_at / LOC150763 / chr2q11.2 / 0.76 / 2.14 / 1.30E-04 / 6.73E-03
228523_at / NANOS1 / chr10q26.11 / 0.76 / 2.14 / 6.63E-06 / 1.05E-03
201939_at / PLK2 / chr5q12.1-q13.2 / 0.76 / 2.13 / 6.60E-06 / 1.05E-03
215356_at / ECAT8 / chr19q13.11 / 0.76 / 2.13 / 3.62E-05 / 2.99E-03
204692_at / LRCH4 / chr7q22 / 0.75 / 2.12 / 7.91E-07 / 3.46E-04
204602_at / DKK1 / chr10q11.2 / 0.75 / 2.12 / 1.62E-03 / 3.31E-02
216370_s_at / TKTL1 / chrXq28 / 0.75 / 2.12 / 5.38E-04 / 1.67E-02
243161_x_at / ZFP42 / chr4q35.2 / 0.75 / 2.11 / 2.05E-04 / 9.02E-03
237737_at / LOC401131 / chr1q12 / 0.75 / 2.11 / 1.81E-04 / 8.38E-03
210467_x_at / MAGEA12 / chrXq28 / 0.74 / 2.10 / 5.35E-06 / 9.50E-04
233413_at / --- / --- / 0.74 / 2.09 / 1.14E-05 / 1.45E-03
223342_at / RRM2B / chr8q23.1 / 0.74 / 2.09 / 5.84E-06 / 1.00E-03
201348_at / GPX3 / chr5q23 / 0.73 / 2.07 / 1.96E-06 / 5.62E-04
240313_at / DMRTB1 / chr1p32.3 / 0.73 / 2.07 / 1.15E-03 / 2.68E-02
202403_s_at / COL1A2 / chr7q22.1 / 0.72 / 2.06 / 4.03E-04 / 1.39E-02
1556499_s_at / COL1A1 / chr17q21.33 / 0.72 / 2.06 / 1.25E-03 / 2.80E-02
217522_at / KCNV2 / chr9p24.2 / 0.72 / 2.06 / 8.92E-06 / 1.26E-03
201666_at / TIMP1 / chrXp11.3-p11.23 / 0.72 / 2.06 / 7.42E-08 / 9.89E-05
201506_at / TGFBI / chr5q31 / 0.72 / 2.05 / 1.75E-03 / 3.47E-02
211538_s_at / HSPA2 / chr14q24.1 / 0.72 / 2.04 / 1.02E-03 / 2.47E-02
208891_at / DUSP6 / chr12q22-q23 / 0.70 / 2.01 / 3.17E-05 / 2.75E-03
207813_s_at / FDXR / chr17q24-q25 / 0.69 / 2.00 / 1.25E-06 / 4.58E-04
209448_at / HTATIP2 / chr11p15.1 / 0.69 / 1.99 / 9.79E-05 / 5.61E-03
219099_at / C12orf5 / chr12p13.3 / 0.68 / 1.97 / 3.37E-06 / 7.53E-04
201744_s_at / LUM / chr12q21.3-q22 / 0.68 / 1.97 / 1.00E-03 / 2.44E-02
215719_x_at / FAS / chr10q24.1 / 0.68 / 1.97 / 3.14E-06 / 7.32E-04
201058_s_at / MYL9 / chr20q11.23 / 0.68 / 1.97 / 2.20E-03 / 3.97E-02
231568_at / RP6-166C19.1 /.. / chrXq24 / 0.68 / 1.96 / 6.64E-07 / 3.04E-04
204239_s_at / NNAT / chr20q11.2-q12 / 0.67 / 1.95 / 1.02E-08 / 4.30E-05
208892_s_at / DUSP6 / chr12q22-q23 / 0.67 / 1.95 / 1.59E-05 / 1.83E-03
210437_at / MAGEA9 / MAGEA9B / chrXq28 / 0.67 / 1.95 / 2.72E-05 / 2.53E-03
215733_x_at / CTAG2 / chrXq28 / 0.66 / 1.94 / 3.19E-06 / 7.40E-04
207534_at / MAGEB1 / chrXp21.3 / 0.66 / 1.94 / 1.19E-06 / 4.49E-04
1555630_a_at / RAB34 / chr17q11.2 / 0.66 / 1.93 / 8.32E-04 / 2.18E-02
220129_at / SOHLH2 / chr13q13.3 / 0.65 / 1.92 / 2.18E-05 / 2.21E-03
206001_at / NPY / chr7p15.1 / 0.65 / 1.91 / 7.02E-04 / 1.97E-02
204780_s_at / FAS / chr10q24.1 / 0.64 / 1.90 / 5.70E-06 / 9.83E-04
211962_s_at / ZFP36L1 / chr14q22-q24 / 0.64 / 1.90 / 1.02E-03 / 2.47E-02
201236_s_at / BTG2 / chr1q32 / 0.64 / 1.89 / 3.08E-06 / 7.25E-04
235700_at / RP13-36C9.1 /.. / chrXq26.3 / 0.64 / 1.89 / 2.63E-05 / 2.49E-03
235456_at / --- / --- / 0.64 / 1.89 / 3.35E-05 / 2.85E-03
33322_i_at / SFN / chr1p36.11 / 0.63 / 1.88 / 1.60E-03 / 3.28E-02
236920_at / PEPP-2 /.. / chrXq24 / 0.62 / 1.87 / 4.61E-07 / 2.56E-04
227687_at / HYLS1 / chr11q24.2 / 0.62 / 1.86 / 6.62E-07 / 3.04E-04
230787_at / --- / --- / 0.62 / 1.86 / 2.99E-08 / 6.40E-05
228834_at / TOB1 / chr17q21 / 0.62 / 1.86 / 1.57E-03 / 3.24E-02
209803_s_at / PHLDA2 / chr11p15.5 / 0.61 / 1.84 / 3.72E-04 / 1.32E-02
202310_s_at / COL1A1 / chr17q21.33 / 0.61 / 1.84 / 1.43E-03 / 3.06E-02
224690_at / C20orf108 / chr20q13.2 / 0.61 / 1.83 / 6.51E-07 / 3.04E-04
204412_s_at / NEFH / chr22q12.2 / 0.60 / 1.83 / 3.18E-03 / 4.98E-02
238935_at / RPS27L / chr15q22.2 / 0.60 / 1.82 / 5.02E-06 / 9.17E-04
226021_at / RDH10 / chr8q21.11 / 0.60 / 1.82 / 1.81E-06 / 5.54E-04
208282_x_at / DAZ1 / DAZ3 /.. / chrYq11.223 / 0.60 / 1.82 / 9.74E-07 / 3.92E-04
1559462_at / --- / --- / 0.59 / 1.81 / 7.97E-05 / 4.93E-03
202704_at / TOB1 / chr17q21 / 0.59 / 1.81 / 2.52E-05 / 2.42E-03
220057_at / XAGE1 /.. / chrXp11.22-p11.21 / chrXp11.22 / 0.59 / 1.81 / 2.71E-05 / 2.53E-03
237956_s_at / LOC133874 / chr5q35.1 / 0.59 / 1.80 / 7.60E-04 / 2.06E-02
209129_at / TRIP6 / chr7q22 / 0.59 / 1.80 / 2.46E-05 / 2.38E-03
214603_at / MAGEA2 / MAGEA2B /.. / chrXq28 / 0.59 / 1.80 / 4.70E-06 / 8.96E-04
229711_s_at / MGC5370 / chr12q14.3 / 0.59 / 1.80 / 8.29E-05 / 5.08E-03
244340_x_at / --- / --- / 0.58 / 1.79 / 1.02E-05 / 1.37E-03
217339_x_at / LOC653387 / chrXq28 / 0.58 / 1.78 / 2.67E-05 / 2.50E-03
1557765_at / LOC643401 / chr5p14.1 / 0.58 / 1.78 / 6.79E-05 / 4.43E-03
226670_s_at / C20orf119 / --- / 0.58 / 1.78 / 1.63E-10 / 2.96E-06
231292_at / EID3 / chr12q23-q24.1 / 0.58 / 1.78 / 2.57E-07 / 1.88E-04
1561754_at / --- / --- / 0.57 / 1.77 / 1.55E-03 / 3.23E-02
224646_x_at / H19 / chr11p15.5 / 0.57 / 1.77 / 1.68E-03 / 3.37E-02
1567912_s_at / RP13-36C9.1 /.. / chrXq26.3 / 0.57 / 1.76 / 1.74E-04 / 8.19E-03
214079_at / DHRS2 / chr14q11.2 / 0.57 / 1.76 / 2.73E-06 / 6.95E-04
231265_at / COX7B2 / chr4p12 / 0.57 / 1.76 / 1.16E-04 / 6.23E-03
208791_at / CLU / chr8p21-p12 / 0.56 / 1.76 / 4.61E-06 / 8.96E-04
226534_at / KITLG / chr12q22 / 0.56 / 1.76 / 6.89E-06 / 1.07E-03
224565_at / TncRNA / chr11q13.1 / 0.56 / 1.76 / 2.09E-04 / 9.18E-03
218641_at / MGC3032 / chr11q13 / 0.56 / 1.75 / 2.46E-08 / 5.86E-05
207169_x_at / DDR1 / chr6p21.3 / 0.56 / 1.75 / 1.67E-08 / 4.89E-05
207663_x_at / GAGE3 / chrXp11.4-p11.2 / 0.56 / 1.75 / 5.68E-06 / 9.83E-04
205829_at / HSD17B1 / chr17q11-q21 / 0.56 / 1.75 / 7.43E-07 / 3.30E-04
219253_at / FAM11B / chr2q14.2 / 0.56 / 1.74 / 4.72E-04 / 1.54E-02
213847_at / PRPH / chr12q12-q13 / 0.56 / 1.74 / 9.77E-05 / 5.61E-03
201060_x_at / STOM / chr9q34.1 / 0.55 / 1.74 / 6.41E-04 / 1.86E-02
221139_s_at / CSAD / chr12q13.11-q14.3 / 0.55 / 1.74 / 6.29E-05 / 4.22E-03
227278_at / --- / --- / 0.55 / 1.74 / 1.87E-05 / 2.02E-03
218346_s_at / SESN1 / chr6q21 / 0.55 / 1.73 / 2.75E-05 / 2.54E-03
204724_s_at / COL9A3 / chr20q13.3 / 0.55 / 1.73 / 5.24E-06 / 9.47E-04
221974_at / PWCR1 / chr15q11.2 / 0.55 / 1.73 / 7.13E-06 / 1.10E-03
204566_at / PPM1D / chr17q23.2 / 0.55 / 1.73 / 7.17E-04 / 1.99E-02
211600_at / --- / --- / 0.54 / 1.72 / 5.96E-04 / 1.79E-02
224589_at / XIST / chrXq13.2 / 0.54 / 1.72 / 2.65E-04 / 1.06E-02
203423_at / RBP1 / chr3q23 / 0.54 / 1.72 / 8.04E-04 / 2.14E-02
204759_at / RCBTB2 / chr13q14.3 / 0.54 / 1.72 / 3.77E-05 / 3.06E-03
210652_s_at / C1orf34 / chr1p32.3 / 0.54 / 1.71 / 4.17E-05 / 3.28E-03
202546_at / VAMP8 / chr2p12-p11.2 / 0.54 / 1.71 / 8.72E-04 / 2.24E-02
205204_at / NMB / chr15q22-qter / 0.53 / 1.70 / 8.83E-07 / 3.71E-04
225160_x_at / MGC5370 / chr12q14.3 / 0.53 / 1.70 / 1.07E-05 / 1.40E-03
1568817_at / --- / --- / 0.53 / 1.70 / 1.32E-05 / 1.60E-03
205386_s_at / MDM2 / chr12q14.3-q15 / 0.53 / 1.70 / 4.78E-04 / 1.55E-02
225762_x_at / LOC284801 / chr20p11.1 / 0.53 / 1.69 / 1.09E-04 / 5.96E-03
238623_at / --- / --- / 0.53 / 1.69 / 2.02E-05 / 2.11E-03
218966_at / MYO5C / chr15q21 / 0.52 / 1.69 / 2.43E-06 / 6.49E-04
208792_s_at / CLU / chr8p21-p12 / 0.52 / 1.68 / 2.68E-05 / 2.51E-03
204867_at / GCHFR / chr15q15 / 0.52 / 1.68 / 2.34E-07 / 1.80E-04
201061_s_at / STOM / chr9q34.1 / 0.52 / 1.68 / 1.17E-03 / 2.70E-02
209806_at / HIST1H2BK / chr6p21.33 / 0.52 / 1.68 / 5.46E-06 / 9.56E-04
209154_at / TAX1BP3 / chr17p13 / 0.52 / 1.68 / 2.16E-07 / 1.79E-04
216252_x_at / FAS / chr10q24.1 / 0.52 / 1.67 / 1.81E-04 / 8.38E-03
210749_x_at / DDR1 / chr6p21.3 / 0.52 / 1.67 / 4.27E-08 / 6.87E-05
209163_at / CYB561 / chr17q11-qter / 0.52 / 1.67 / 1.36E-03 / 2.97E-02
218627_at / DRAM / chr12q23.2 / 0.51 / 1.67 / 3.31E-06 / 7.47E-04
231339_at / TSPYL6 / chr2p16.2 / 0.51 / 1.67 / 1.29E-04 / 6.68E-03
223204_at / C4orf18 / chr4q32.1 / 0.51 / 1.67 / 1.80E-04 / 8.35E-03
218634_at / PHLDA3 / chr1q31 / 0.51 / 1.67 / 2.25E-05 / 2.25E-03
243612_at / NSD1 / chr5q35.2-q35.3 / 0.51 / 1.66 / 3.71E-05 / 3.03E-03
220325_at / TAF7L / chrXq22.1 / 0.51 / 1.66 / 1.36E-03 / 2.97E-02
220136_s_at / CRYBA2 / chr2q34-q36 / 0.51 / 1.66 / 5.12E-05 / 3.74E-03
206626_x_at / SSX1 /// LOC652630 / chrXp11.23-p11.22 / 0.51 / 1.66 / 6.26E-05 / 4.21E-03
201117_s_at / CPE / chr4q32.3 / 0.51 / 1.66 / 4.86E-05 / 3.63E-03
214157_at / GNAS / chr20q13.3 / 0.51 / 1.66 / 1.21E-03 / 2.75E-02
218007_s_at / RPS27L / chr15q22.2 / 0.50 / 1.66 / 2.04E-05 / 2.12E-03
224558_s_at / MALAT1 / chr11q13.1 / 0.50 / 1.65 / 1.76E-04 / 8.25E-03
204781_s_at / FAS / chr10q24.1 / 0.50 / 1.65 / 1.83E-05 / 2.00E-03
204268_at / S100A2 / chr1q21 / 0.50 / 1.65 / 9.69E-04 / 2.40E-02
228875_at / C6orf189 / chr6q22.2 / 0.50 / 1.65 / 3.03E-04 / 1.16E-02
224710_at / RAB34 / chr17q11.2 / 0.50 / 1.64 / 1.95E-03 / 3.70E-02
225841_at / C1orf59 / chr1p13.3 / 0.49 / 1.64 / 9.88E-05 / 5.65E-03
208949_s_at / LGALS3/GALIG / chr14q21-q22 / 0.49 / 1.64 / 1.02E-04 / 5.76E-03
227785_at / SDCCAG8 / chr1q43-q44 / 0.49 / 1.64 / 1.54E-07 / 1.38E-04
219463_at / C20orf103 / chr20p12 / 0.49 / 1.63 / 2.81E-05 / 2.58E-03
74694_s_at / RABEP2 /.. / chr16p11.2 / 0.49 / 1.63 / 9.67E-07 / 3.92E-04
44783_s_at / HEY1 / chr8q21 / 0.49 / 1.62 / 4.04E-06 / 8.37E-04
224380_s_at / TAF7L / chrXq22.1 / 0.48 / 1.62 / 2.06E-03 / 3.82E-02
202708_s_at / HIST2H2BE / chr1q21-q23 / 0.48 / 1.62 / 6.07E-07 / 3.00E-04
226591_at / --- / --- / 0.48 / 1.62 / 5.45E-06 / 9.56E-04
242350_s_at / ST8SIA6 / chr10p12.33 / 0.48 / 1.62 / 3.49E-08 / 6.58E-05
203180_at / ALDH1A3 / chr15q26.3 / 0.48 / 1.61 / 1.09E-04 / 5.96E-03
201721_s_at / LAPTM5 / chr1p34 / 0.47 / 1.61 / 1.17E-05 / 1.47E-03
226587_at / --- / --- / 0.47 / 1.60 / 1.24E-04 / 6.54E-03
205174_s_at / QPCT / chr2p22.2 / 0.47 / 1.60 / 2.55E-04 / 1.04E-02
227134_at / SYTL1 / chr1p36.11 / 0.47 / 1.60 / 2.52E-04 / 1.03E-02
1552906_at / FMR1NB / chrXq27.3-q28 / 0.47 / 1.60 / 7.93E-04 / 2.12E-02
242346_x_at / --- / --- / 0.47 / 1.60 / 1.17E-04 / 6.26E-03
204014_at / DUSP4 / chr8p12-p11 / 0.47 / 1.60 / 1.16E-04 / 6.21E-03
239303_at / --- / --- / 0.47 / 1.60 / 1.23E-06 / 4.55E-04
223551_at / PKIB / chr6q22.31 / 0.47 / 1.60 / 6.84E-05 / 4.44E-03
210058_at / MAPK13 / chr6p21.31 / 0.47 / 1.59 / 3.05E-07 / 2.01E-04
202291_s_at / MGP / chr12p13.1-p12.3 / 0.47 / 1.59 / 4.28E-04 / 1.45E-02
202957_at / HCLS1 / chr3q13 / 0.46 / 1.59 / 6.98E-04 / 1.96E-02
208779_x_at / DDR1 / chr6p21.3 / 0.46 / 1.59 / 9.22E-08 / 1.10E-04
203407_at / PPL / chr16p13.3 / 0.46 / 1.59 / 1.70E-08 / 4.89E-05
238299_at / LASS5 / chr12q13.13 / 0.46 / 1.59 / 2.97E-06 / 7.12E-04
202814_s_at / HEXIM1 / chr17q21.31 / 0.46 / 1.58 / 1.89E-06 / 5.59E-04
223883_s_at / STK31 / chr7p15.3 / 0.46 / 1.58 / 8.88E-05 / 5.28E-03
203409_at / DDB2 / chr11p12-p11 / 0.46 / 1.58 / 1.16E-03 / 2.69E-02
209295_at / TNFRSF10B / chr8p22-p21 / 0.46 / 1.58 / 5.08E-04 / 1.62E-02
228285_at / TDRD9 / chr14q32.33 / 0.45 / 1.58 / 2.17E-05 / 2.20E-03
223687_s_at / LY6K / chr8q24.3 / 0.45 / 1.58 / 3.16E-04 / 1.19E-02
210059_s_at / MAPK13 / chr6p21.31 / 0.45 / 1.57 / 8.88E-10 / 6.94E-06
223484_at / C15orf48 / chr15q21.1 / 0.45 / 1.57 / 2.44E-04 / 1.01E-02
208933_s_at / --- / --- / 0.45 / 1.57 / 4.91E-05 / 3.64E-03
206546_at / SYCP2 / chr20q13.33 / 0.45 / 1.57 / 1.95E-04 / 8.77E-03
1553185_at / RASEF / chr9q21.32 / 0.45 / 1.57 / 1.99E-04 / 8.88E-03
223908_at / HDAC8 / chrXq13 / 0.45 / 1.57 / 7.83E-07 / 3.45E-04
222016_s_at / ZNF323 / --- / 0.45 / 1.57 / 1.09E-05 / 1.41E-03
235760_at / --- / --- / 0.45 / 1.56 / 4.63E-07 / 2.56E-04
207325_x_at / MAGEA1 / chrXq28 / 0.45 / 1.56 / 1.04E-07 / 1.11E-04
204416_x_at / APOC1 / chr19q13.2 / 0.45 / 1.56 / 1.39E-04 / 6.99E-03
211340_s_at / MCAM / chr11q23.3 / 0.45 / 1.56 / 1.06E-04 / 5.91E-03
214091_s_at / GPX3 / chr5q23 / 0.45 / 1.56 / 6.63E-06 / 1.05E-03
241262_at / YY1AP1 / chr1q22 / 0.44 / 1.56 / 1.68E-06 / 5.36E-04
204810_s_at / CKM / chr19q13.2-q13.3 / 0.44 / 1.56 / 2.79E-04 / 1.10E-02
212203_x_at / IFITM3 / chr11p15.5 / 0.44 / 1.56 / 4.67E-04 / 1.53E-02
202411_at / IFI27 / chr14q32 / 0.44 / 1.55 / 1.88E-03 / 3.62E-02
230388_s_at / LOC644246 /.. / chr17q21.31 / 0.44 / 1.55 / 8.89E-07 / 3.71E-04
226034_at / --- / --- / 0.44 / 1.55 / 1.94E-05 / 2.06E-03
1557060_at / LOC148756 / chr1q25.3 / 0.44 / 1.55 / 3.63E-04 / 1.29E-02
209628_at / NXT2 / chrXq22.3 / 0.44 / 1.55 / 6.35E-04 / 1.85E-02
200800_s_at / HSPA1A / HSPA1B / chr6p21.3 / 0.44 / 1.55 / 2.02E-03 / 3.79E-02
237435_at / --- / --- / 0.43 / 1.54 / 2.55E-03 / 4.35E-02
209260_at / SFN / chr1p36.11 / 0.43 / 1.54 / 1.71E-03 / 3.42E-02
212980_at / USP34 / chr2p15 / 0.43 / 1.54 / 4.08E-07 / 2.45E-04
204015_s_at / DUSP4 / chr8p12-p11 / 0.43 / 1.54 / 5.21E-05 / 3.76E-03
228315_at / --- / --- / 0.43 / 1.54 / 1.33E-03 / 2.93E-02
1555396_s_at / LOC340602 / chrXp11.22 / 0.43 / 1.54 / 2.65E-05 / 2.50E-03
226150_at / PPAPDC1B / chr8p12 / 0.43 / 1.53 / 1.19E-05 / 1.48E-03
203619_s_at / FAIM2 / chr12q13 / 0.43 / 1.53 / 1.36E-05 / 1.64E-03
201581_at / TXNDC13 / chr20p12 / 0.43 / 1.53 / 5.43E-05 / 3.86E-03
227221_at / --- / --- / 0.43 / 1.53 / 6.21E-04 / 1.84E-02
223723_at / MFI2 / chr3q28-q29 / 0.43 / 1.53 / 7.47E-06 / 1.12E-03
217542_at / CPM / chr12q14.3 / 0.43 / 1.53 / 4.11E-04 / 1.41E-02
209375_at / XPC / chr3p25 / 0.43 / 1.53 / 2.77E-06 / 6.97E-04
1007_s_at / DDR1 / chr6p21.3 / 0.42 / 1.53 / 2.20E-08 / 5.72E-05
227711_at / FAM112B / chr12q13.2 / 0.42 / 1.53 / 8.41E-04 / 2.19E-02
207260_at / FEV / chr2q36 / 0.42 / 1.53 / 4.68E-05 / 3.56E-03
231863_at / ING3 / chr7q31 / 0.42 / 1.53 / 2.43E-03 / 4.23E-02
201331_s_at / STAT6 / chr12q13 / 0.42 / 1.53 / 1.09E-05 / 1.41E-03
214642_x_at / MAGEA5 / chrXq28 / 0.42 / 1.53 / 1.04E-05 / 1.38E-03
205932_s_at / MSX1 / chr4p16.3-p16.1 / 0.42 / 1.53 / 2.80E-04 / 1.10E-02
224997_x_at / H19 / chr11p15.5 / 0.42 / 1.53 / 1.08E-03 / 2.57E-02
1552858_at / MAGEB6 / chrXp21.3 / 0.42 / 1.53 / 3.16E-04 / 1.19E-02
217890_s_at / PARVA / chr11p15.3 / 0.42 / 1.53 / 1.09E-06 / 4.26E-04
211379_x_at / B3GALNT1 / chr3q25 / 0.42 / 1.52 / 2.12E-04 / 9.20E-03
218435_at / DNAJC15 / chr13q14.1 / 0.42 / 1.52 / 3.02E-04 / 1.16E-02
222455_s_at / PARVA / chr11p15.3 / 0.42 / 1.52 / 4.47E-09 / 2.22E-05
210589_s_at / GBA /// GBAP / chr1q21 / 0.42 / 1.52 / 3.77E-06 / 8.03E-04
218611_at / IER5 / chr1q25.3 / 0.42 / 1.52 / 2.82E-04 / 1.10E-02
201580_s_at / TXNDC13 / chr20p12 / 0.42 / 1.52 / 3.00E-06 / 7.12E-04
219628_at / ZMAT3 / chr3q26.3-q27 / 0.41 / 1.51 / 2.00E-04 / 8.91E-03
1553186_x_at / RASEF / chr9q21.32 / 0.41 / 1.51 / 5.27E-04 / 1.65E-02
1556244_s_at / LOC375196 / chr2p22.3 / 0.41 / 1.51 / 5.42E-05 / 3.86E-03
202283_at / SERPINF1 / chr17p13.1 / 0.41 / 1.51 / 7.33E-04 / 2.02E-02
225512_at / ZBTB38 / chr3q23 / 0.41 / 1.51 / 3.35E-04 / 1.23E-02
238127_at / GAS6 / chr13q34 / 0.41 / 1.51 / 9.59E-05 / 5.54E-03
234983_at / --- / --- / 0.41 / 1.50 / 9.42E-08 / 1.10E-04
210519_s_at / NQO1 / chr16q22.1 / 0.41 / 1.50 / 5.11E-04 / 1.63E-02
210503_at / MAGEA11 / chrXq28 / 0.41 / 1.50 / 3.63E-05 / 2.99E-03
207909_x_at / DAZ1 / DAZ3 /.. / chrYq11.223 / 0.41 / 1.50 / 1.53E-06 / 5.23E-04
219928_s_at / CABYR / chr18q11.2 / 0.41 / 1.50 / 3.99E-06 / 8.32E-04
227870_at / NOPE / chr15q22.31 / 0.41 / 1.50 / 4.25E-07 / 2.46E-04
204608_at / ASL / chr7cen-q11.2 / 0.41 / 1.50 / 1.52E-05 / 1.77E-03
4b) Probes downregulated by DAC and TSA treatment (>1.5 FC, adj. ) in NBL cell lines
ID / Gene Symbol / Chromosomal Location / logFC / FC / 1/FC / P.Value / adj.P.Val1553575_at / --- / --- / -0.98 / 0.38 / 2.65 / 5.93E-06 / 1.01E-03
201626_at / INSIG1 / chr7q36 / -0.93 / 0.40 / 2.52 / 9.64E-07 / 3.92E-04
221879_at / CALML4 / chr15q23 / -0.87 / 0.42 / 2.39 / 1.40E-07 / 1.30E-04
64408_s_at / CALML4 / chr15q23 / -0.82 / 0.44 / 2.27 / 3.97E-08 / 6.58E-05
201627_s_at / INSIG1 / chr7q36 / -0.82 / 0.44 / 2.27 / 2.73E-07 / 1.94E-04
209146_at / SC4MOL / chr4q32-q34 / -0.76 / 0.47 / 2.13 / 8.68E-05 / 5.23E-03
210567_s_at / SKP2 / chr5p13 / -0.74 / 0.48 / 2.09 / 5.22E-10 / 4.75E-06
202068_s_at / LDLR / chr19p13.3 / -0.72 / 0.49 / 2.06 / 5.92E-06 / 1.01E-03
200832_s_at / SCD / chr10q23-q24 / -0.72 / 0.49 / 2.06 / 1.15E-06 / 4.38E-04
205822_s_at / HMGCS1 / chr5p14-p13 / -0.69 / 0.50 / 2.00 / 3.15E-05 / 2.75E-03
204646_at / DPYD / chr1p22 / -0.66 / 0.52 / 1.94 / 8.09E-06 / 1.17E-03
225520_at / MTHFD1L / chr6q25.1 / -0.66 / 0.52 / 1.93 / 1.73E-07 / 1.49E-04
221750_at / HMGCS1 / chr5p14-p13 / -0.65 / 0.52 / 1.92 / 1.78E-04 / 8.30E-03
228049_x_at / --- / --- / -0.64 / 0.53 / 1.89 / 9.67E-07 / 3.92E-04
223839_s_at / --- / --- / -0.64 / 0.53 / 1.89 / 1.32E-05 / 1.60E-03
204338_s_at / RGS4 / chr1q23.3 / -0.63 / 0.53 / 1.88 / 2.45E-05 / 2.38E-03
231850_x_at / KIAA1712 / chr4q34 / -0.63 / 0.53 / 1.87 / 2.94E-05 / 2.64E-03
204690_at / STX8 / chr17p12 / -0.62 / 0.54 / 1.87 / 1.36E-08 / 4.89E-05
201397_at / PHGDH / chr1p12 / -0.60 / 0.55 / 1.82 / 4.46E-09 / 2.22E-05
212739_s_at / NME4 / chr16p13.3 / -0.59 / 0.55 / 1.81 / 4.84E-08 / 7.35E-05
204120_s_at / ADK / chr10q22|10q11-q24 / -0.59 / 0.55 / 1.81 / 6.19E-07 / 3.00E-04
210950_s_at / FDFT1 / chr8p23.1-p22 / -0.58 / 0.56 / 1.79 / 1.64E-05 / 1.86E-03
204868_at / ICT1 / chr17q25.1 / -0.58 / 0.56 / 1.79 / 1.70E-06 / 5.38E-04
204337_at / RGS4 / chr1q23.3 / -0.57 / 0.57 / 1.76 / 7.79E-06 / 1.15E-03
227059_at / GPC6 / chr13q32 / -0.57 / 0.57 / 1.76 / 3.69E-06 / 7.97E-04
228334_x_at / KIAA1712 / chr4q34 / -0.57 / 0.57 / 1.76 / 7.49E-05 / 4.73E-03
206103_at / RAC3 / chr17q25.3 / -0.57 / 0.57 / 1.76 / 3.90E-08 / 6.58E-05
235570_at / --- / --- / -0.56 / 0.57 / 1.74 / 3.13E-07 / 2.04E-04
227963_at / C17orf45 / chr17p11.2 / -0.55 / 0.57 / 1.74 / 4.64E-05 / 3.53E-03
204805_s_at / H1FX / chr3q21.3 / -0.55 / 0.58 / 1.73 / 1.03E-05 / 1.38E-03
208700_s_at / TKT / chr3p14.3 / -0.55 / 0.58 / 1.73 / 5.32E-08 / 7.84E-05
201625_s_at / INSIG1 / chr7q36 / -0.54 / 0.58 / 1.72 / 8.72E-07 / 3.69E-04
223114_at / COQ5 / chr12q24.31 / -0.53 / 0.59 / 1.70 / 6.71E-06 / 1.06E-03
208647_at / FDFT1 / chr8p23.1-p22 / -0.53 / 0.59 / 1.70 / 1.71E-04 / 8.07E-03
219188_s_at / LRP16 / chr11q11 / -0.53 / 0.59 / 1.70 / 2.58E-05 / 2.45E-03
219148_at / PBK / chr8p21.2 / -0.53 / 0.59 / 1.69 / 8.73E-05 / 5.25E-03
218788_s_at / SMYD3 / chr1q44 / -0.52 / 0.59 / 1.69 / 2.52E-06 / 6.58E-04
204339_s_at / RGS4 / chr1q23.3 / -0.52 / 0.59 / 1.69 / 2.61E-05 / 2.48E-03
241789_at / --- / --- / -0.51 / 0.60 / 1.67 / 6.12E-07 / 3.00E-04
201275_at / FDPS / chr1q22 / -0.51 / 0.60 / 1.67 / 1.15E-04 / 6.18E-03
208699_x_at / TKT / chr3p14.3 / -0.51 / 0.60 / 1.67 / 7.72E-08 / 1.00E-04
214437_s_at / SHMT2 / chr12q12-q14 / -0.51 / 0.60 / 1.67 / 2.79E-08 / 6.36E-05
203006_at / INPP5A / chr10q26.3 / -0.51 / 0.60 / 1.66 / 4.43E-08 / 6.92E-05
238447_at / RBMS3 / chr3p24-p23 / -0.50 / 0.60 / 1.65 / 4.81E-06 / 9.04E-04
204119_s_at / ADK / chr10q22|10q11-q24 / -0.49 / 0.61 / 1.63 / 5.31E-07 / 2.82E-04
219301_s_at / CNTNAP2 / chr7q35-q36 / -0.48 / 0.62 / 1.62 / 2.26E-05 / 2.25E-03
203690_at / TUBGCP3 / chr13q34 / -0.48 / 0.62 / 1.62 / 5.96E-06 / 1.01E-03
210683_at / NRTN / chr19p13.3 / -0.48 / 0.62 / 1.62 / 9.38E-06 / 1.29E-03
225834_at / LOC652689 /.. / chr1q32.1 /.. / -0.48 / 0.62 / 1.61 / 1.41E-04 / 7.04E-03
205047_s_at / ASNS / chr7q21.3 / -0.48 / 0.62 / 1.61 / 3.83E-04 / 1.34E-02
240419_at / SLC6A15 / chr12q21.3 / -0.47 / 0.62 / 1.60 / 1.12E-06 / 4.30E-04
227069_at / CUTL1 / chr7q22.1 / -0.47 / 0.62 / 1.60 / 2.41E-05 / 2.35E-03
228606_at / MGC33212 / chr3q29 / -0.47 / 0.63 / 1.60 / 4.14E-06 / 8.42E-04
219077_s_at / WWOX / chr16q23.3-q24.1 / -0.47 / 0.63 / 1.60 / 1.06E-07 / 1.11E-04
217988_at / CCNB1IP1 / chr14q11.2 / -0.46 / 0.63 / 1.58 / 2.01E-05 / 2.10E-03
224610_at / STX5 / chr11q12.3 / -0.46 / 0.63 / 1.58 / 3.69E-05 / 3.02E-03
211708_s_at / SCD / chr10q23-q24 / -0.46 / 0.63 / 1.58 / 6.75E-05 / 4.43E-03
219819_s_at / MRPS28 / chr8q21.1-q21.2 / -0.46 / 0.63 / 1.58 / 2.84E-06 / 7.07E-04
203029_s_at / PTPRN2 / chr7q36 / -0.46 / 0.63 / 1.58 / 1.08E-03 / 2.56E-02
219264_s_at / PPP2R3B / chrXp22.33; Yp11.3 / -0.45 / 0.63 / 1.58 / 5.64E-09 / 2.57E-05
201790_s_at / DHCR7 / chr11q13.2-q13.5 / -0.45 / 0.64 / 1.57 / 8.53E-06 / 1.22E-03
205967_at / HIST1H4C / chr6p21.3 / -0.45 / 0.64 / 1.57 / 1.88E-03 / 3.62E-02
212609_s_at / AKT3 / chr1q43-q44 / -0.45 / 0.64 / 1.57 / 2.51E-06 / 6.58E-04
1555501_s_at / RSRC1 / chr3q25.32 / -0.45 / 0.64 / 1.56 / 2.41E-08 / 5.86E-05
214095_at / SHMT2 / chr12q12-q14 / -0.45 / 0.64 / 1.56 / 2.94E-06 / 7.12E-04
214280_x_at / HNRPA1 / chr12q13.1 / -0.45 / 0.64 / 1.56 / 2.93E-05 / 2.64E-03
232263_at / SLC6A15 / chr12q21.3 / -0.44 / 0.64 / 1.56 / 9.21E-06 / 1.28E-03
202539_s_at / HMGCR / chr5q13.3-q14 / -0.44 / 0.64 / 1.56 / 9.71E-04 / 2.40E-02
229097_at / DIAPH3 / chr13q21.2 / -0.44 / 0.64 / 1.56 / 5.56E-05 / 3.89E-03
228555_at / CAMK2D / chr4q26 / -0.44 / 0.64 / 1.55 / 2.71E-07 / 1.94E-04
223319_at / GPHN / chr14q23.3 / -0.44 / 0.65 / 1.55 / 3.92E-08 / 6.58E-05
227044_at / TBC1D22A / chr22q13.3 / -0.43 / 0.65 / 1.54 / 1.11E-05 / 1.43E-03
229459_at / FAM19A5 / chr22q13.32 / -0.43 / 0.65 / 1.54 / 4.35E-05 / 3.35E-03
200831_s_at / SCD / chr10q23-q24 / -0.43 / 0.65 / 1.54 / 8.71E-06 / 1.23E-03
225399_at / C1orf19 / chr1q25 / -0.43 / 0.65 / 1.54 / 3.97E-06 / 8.32E-04
228240_at / --- / --- / -0.43 / 0.65 / 1.54 / 1.59E-06 / 5.27E-04
206445_s_at / PRMT1 / chr19q13.3 / -0.43 / 0.65 / 1.54 / 9.65E-08 / 1.10E-04
242828_at / FIGN / chr2q24.3 / -0.43 / 0.65 / 1.53 / 5.06E-05 / 3.72E-03
205677_s_at / DLEU1 /.. / chr13q14.3 /.. / -0.42 / 0.65 / 1.53 / 2.48E-06 / 6.57E-04
205373_at / CTNNA2 / chr2p12-p11.1 / -0.42 / 0.66 / 1.53 / 7.02E-05 / 4.52E-03
204875_s_at / GMDS / chr6p25 / -0.42 / 0.66 / 1.53 / 3.80E-07 / 2.39E-04
200779_at / ATF4 / chr22q13.1 / -0.42 / 0.66 / 1.53 / 1.63E-06 / 5.33E-04
208886_at / H1F0 / chr22q13.1 / -0.42 / 0.66 / 1.53 / 7.36E-06 / 1.12E-03
223015_at / EIF2A / chr3q25.1 / -0.42 / 0.66 / 1.53 / 1.47E-05 / 1.74E-03
215739_s_at / TUBGCP3 / chr13q34 / -0.42 / 0.66 / 1.52 / 4.74E-06 / 8.99E-04
222209_s_at / TMEM135 / chr11q14.2 / -0.42 / 0.66 / 1.52 / 1.37E-05 / 1.65E-03
211998_at / H3F3B / chr17q25 / -0.42 / 0.66 / 1.52 / 1.07E-04 / 5.93E-03
214096_s_at / SHMT2 / chr12q12-q14 / -0.42 / 0.66 / 1.52 / 4.35E-06 / 8.72E-04
212175_s_at / AK2 / chr1p34 / -0.41 / 0.66 / 1.51 / 3.54E-07 / 2.25E-04
217294_s_at / ENO1 / chr1p36.3-p36.2 / -0.41 / 0.66 / 1.51 / 1.12E-04 / 6.03E-03
238015_at / LOC201725 / chr4q32.1 / -0.41 / 0.66 / 1.51 / 7.50E-06 / 1.13E-03
204283_at / FARS2 / chr6p25.1 / -0.41 / 0.66 / 1.51 / 8.39E-08 / 1.07E-04
211162_x_at / SCD / chr10q23-q24 / -0.41 / 0.66 / 1.51 / 9.38E-05 / 5.47E-03
224478_s_at / MGC11257 / chr7p22.3 / -0.41 / 0.66 / 1.51 / 1.90E-05 / 2.03E-03
216620_s_at / ARHGEF10 / chr8p23 / -0.41 / 0.66 / 1.51 / 1.17E-08 / 4.56E-05
223171_at / DYM / chr18q12-q21.1 / -0.41 / 0.66 / 1.51 / 6.31E-08 / 8.84E-05
214862_x_at / --- / --- / -0.41 / 0.67 / 1.50 / 3.99E-05 / 3.19E-03
Supplementary Table 5Treatment effect of DAC and TSA on gene expression of PNET cell lines
5a)Top list probe sets upregulated by DAC and TSA treatment (>1.5 FC, adj. P.val<0.05) in PNET cell lines. In bold genes which show significant demethylation of a promoter located methylation probe.
ID / Gene Symbol / Chromosomal Location / logFC / FC / P.Value / adj.P.Val220057_at / XAGE1 /.. / chrXp11.22-p11.21 / chrXp11.22 / 3.08 / 21.80 / 1.55E-08 / 8.48E-04
220784_s_at / UTS2 / chr1p36 / 2.67 / 14.43 / 8.08E-07 / 1.47E-02
1556395_at / --- / --- / 2.56 / 12.96 / 1.91E-05 / 3.73E-02
231307_at / PAGE2 / chrXp11.21 / 2.23 / 9.27 / 6.48E-06 / 2.97E-02
210497_x_at / SSX2 /.. / chrXp11.23-p11.22 / chrXp11.22 / 1.90 / 6.70 / 3.94E-06 / 2.69E-02
225681_at / CTHRC1 / chr8q22.3 / 1.85 / 6.37 / 1.91E-05 / 3.73E-02
210394_x_at / SSX4 /.. / chrXp11.23 / 1.80 / 6.08 / 1.03E-05 / 3.66E-02
208792_s_at / CLU / chr8p21-p12 / 1.60 / 4.96 / 3.69E-06 / 2.69E-02
208791_at / CLU / chr8p21-p12 / 1.57 / 4.83 / 9.42E-06 / 3.66E-02
206626_x_at / SSX1 /.. / chrXp11.23-p11.22 / 1.54 / 4.67 / 1.27E-05 / 3.66E-02
207666_x_at / SSX3 / chrXp11.23 / 1.44 / 4.20 / 6.51E-06 / 2.97E-02
211425_x_at / SSX4 /.. / chrXp11.23 / 1.37 / 3.93 / 1.91E-05 / 3.73E-02
205932_s_at / MSX1 / chr4p16.3-p16.1 / 1.28 / 3.61 / 6.46E-07 / 1.47E-02
204149_s_at / GSTM4 / chr1p13.3 / 1.08 / 2.93 / 1.23E-05 / 3.66E-02
209710_at / GATA2 / chr3q21.3 / 0.99 / 2.69 / 6.29E-06 / 2.97E-02
55081_at / MICAL-L1 / chr22q13.1-q13.2 / 0.98 / 2.65 / 5.09E-06 / 2.97E-02
223551_at / PKIB / chr6q22.31 / 0.96 / 2.62 / 1.23E-06 / 1.68E-02
217339_x_at / LOC653387 / chrXq28 / 0.85 / 2.34 / 1.85E-05 / 3.73E-02
204855_at / SERPINB5 / chr18q21.3 / 0.82 / 2.28 / 1.76E-06 / 1.92E-02
204937_s_at / ZNF274 / chr19qter / 0.82 / 2.26 / 2.74E-05 / 4.69E-02
219681_s_at / RAB11FIP1 / chr8p11.22 / 0.82 / 2.26 / 1.72E-05 / 3.73E-02
222043_at / CLU / chr8p21-p12 / 0.78 / 2.18 / 3.02E-05 / 4.75E-02
221666_s_at / PYCARD / chr16p12-p11.2 / 0.74 / 2.09 / 1.03E-05 / 3.66E-02
31845_at / ELF4 / chrXq26 / 0.70 / 2.01 / 2.54E-05 / 4.49E-02
74694_s_at / RABEP2 /.. / chr16p11.2 / 0.69 / 2.00 / 2.01E-05 / 3.79E-02
209087_x_at / MCAM / chr11q23.3 / 0.68 / 1.97 / 2.55E-05 / 4.49E-02
221873_at / ZNF143 / chr11p15.4 / 0.68 / 1.96 / 3.59E-06 / 2.69E-02
1568619_s_at / LOC162073 / chr16p12.3 / 0.65 / 1.92 / 1.38E-05 / 3.73E-02
221779_at / MICAL-L1 / chr22q13.1-q13.2 / 0.65 / 1.91 / 1.44E-05 / 3.73E-02
210869_s_at / MCAM / chr11q23.3 / 0.60 / 1.82 / 1.84E-05 / 3.73E-02
5b) Probe sets downregulated by DAC and TSA treatment (>1.5 FC, adj. P.val<0.05) in PNET cell lines
ID / Gene Symbol / Chromosomal Location / logFC / FC / P.Value / adj.P.Val219528_s_at / BCL11B / chr14q32.2 / -0.92 / 0.40 / 3.04E-05 / 4.75E-02
223839_s_at / --- / --- / -0.87 / 0.42 / 1.20E-05 / 3.66E-02
200832_s_at / SCD / chr10q23-q24 / -0.78 / 0.46 / 3.02E-05 / 4.75E-02
219188_s_at / LRP16 / chr11q11 / -0.76 / 0.47 / 1.08E-05 / 3.66E-02
225457_s_at / LOC25845 / chr5p15.33 / -0.57 / 0.56 / 1.79E-05 / 3.73E-02