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Table 1 Histone transcripts show altered levels following silencing of CASP8AP2/FLASH

From: Systems-wide RNAi analysis of CASP8AP2/FLASH shows transcriptional deregulation of the replication-dependent histone genes and extensive effects on the transcriptome of colorectal cancer cells

Ref Seq Gene Symbol Chromosomal position Agilent Probe CASP8AP2/FLASH SILENCED SW480 cells Published HeLa data
     Fold change (Log 2 ) siCASP8AP2.3 q values
siCASP8AP2.3
Fold change (Log 2 ) siCASP8AP2.6 q values
siCASP8AP2.6
Narita et al Shepard et al PAS seq #
NM_012115 CASP8AP2 chr6:90640368-90640427 A_23_P58898 -2.06 6.28E-15 -1.81 6.14E-13 - -
NM_003548 HIST2H4A/
HIST2H4B
chr1:146617469-146617528 A_23_P436281 3.01 1.21E-20 2.61 4.73E-18   chr1 - 148098952-1
NM_003516 HIST2H2AA3/ chr1:146635701-146635760 A_23_P309381 3.80 9.00E-09 4.24 4.19E-10 Yes*  
  HIST2H2AA4         
NM_003516 HIST2H2AA3/1 chr1:146636178-146636234 A_23_P103981 3.83 3.55E-11 3.72 8.65E-11   
  HIST2H2AA4         
NM_003528 HIST2H2BE chr1:146669546-146669487 A_24_P148321 3.78 5.33E-13 3.63 1.93E-12   chr1-148122634-6, chr-148124269-1, chr1-148124357-1
NM_003528 HIST2H2BE chr1:146670196-146670137 A_23_P149545 2.24 8.74E-14 2.39 7.62E-15   
NM_003528 HIST2H2BE2 chr1:146671162-146671103 A_24_P156911 3.52 6.07E-19 3.49 7.82E-19   
NM_003517 HIST2H2AC chr1:146671911-146671970 A_24_P8721 3.17 3.73E-16 2.97 3.91E-15   chr1-148125568-4
NM_003517 HIST2H2AC chr1:146671936-146671995 A_23_P301247 -1.90 8.19E-10 -2.02 1.36E-10   
NM_175065 HIST2H2AB chr1:146672317-146672258 A_24_P68631 3.88 1.18E-17 3.77 3.43E-17   
NM_033445 HIST3H2A chr1:224952044-224951985 A_23_P149301 3.10 1.82E-16 3.17 7.19E-17   
NM_175055 HIST3H2BB chr1:224952760-224952819 A_23_P332992 3.50 2.92E-16 3.42 6.04E-16   
NM_003537 HIST1H3B chr6:26139947-26139888 A_24_P174924 1.57 9.00E-06 1.12 1.50E-03   
NM_003537 HIST1H3B chr6:26139960-26139901 A_23_P93258 3.48 1.00E-13 3.31 5.69E-13   
NM_003513 HIST1H2AB chr6:26141499-26141440 A_24_P223384 1.93 3.63E-10 1.95 2.41E-10   
NM_021062 HIST1H2BB chr6:26151544-26151485 A_23_P111054 3.14 2.36E-15 2.93 2.72E-14   
NM_005319 HIST1H1C chr6:26164088-26164029 A_23_P122443 3.33 1.27E-13 3.40 5.92E-14 Yes  
NM_003526 HIST1H2BC chr6:26232021-26231962 A_23_P93180 3.36 5.81E-17 3.30 1.03E-16   
NM_005321 HIST1H1E chr6:26264907-26264966 A_23_P7976 3.35 1.45E-13 3.15 1.18E-12   chr6-26265322-1
NM_0210633 HIST1H2BD chr6:26266453-26266512 A_24_P146211 3.87 1.47E-19 3.77 4.38E-19 Yes ch6-26279217-1, ch6-26279551-20, chr6-26266834-7
NM_003523 HIST1H2BE chr6:26292319-26292378 A_23_P30776 3.42 2.47E-16 3.44 1.72E-16 Yes  
NM_003530 HIST1H3D chr6:26305256-26305197 A_23_P219045 3.82 1.30E-14 3.83 1.10E-14   
NM_003530 HIST1H3D chr6:26305296-26305237 A_24_P217834 2.99 3.58E-13 3.09 1.01E-13   
NM_021065 HIST1H2AD4 chr6:26307121-26307062 A_23_P428184 4.23 6.78E-16 4.21 6.99E-16   
NM_003522 HIST1H2BF chr6:26308082-26308141 A_23_P42178 3.44 3.50E-16 3.41 4.47E-16 Yes  
NM_003518 HIST1H2BG chr6:26324755-26324696 A_23_P167997 3.93 1.29E-20 3.78 6.51E-20   chr6-26324393-2
NM_021052 HIST1H2AE chr6:26325533-26325592 A_23_P59045 4.32 9.87E-24 3.90 7.90E-22 Yes chr6-26325683-13
NM_005320 HIST1H1D chr6:26342737-26342678 A_24_P260639 3.59 1.39E-13 3.22 5.45E-12   
NM_003540 HIST1H4F chr6:26348797-26348856 A_23_P359540 2.78 1.14E-16 2.44 1.42E-14   
NM_021018 HIST1H3F chr6:26358626-26358567 A_23_P30799 3.36 2.65E-14 3.15 2.41E-13   chr6-26358379-1
NM_003524 HIST1H2BH chr6:26360201-26360260 A_23_P366216 3.19 4.08E-16 3.04 2.19E-15 Yes chr6-26360284-3
BC0121855 HIST1H3G chr6:26377826-26377767 A_32_P794894 3.07 7.43E-30 3.54 8.23E-33   
NM_003534 HIST1H3G chr6:26379448-26379389 A_23_P42198 1.15 1.39E-04 1.27 3.34E-05   
NM_003525 HIST1H2BI chr6:26381354-26381413 A_23_P111041 3.51 7.27E-15 3.69 1.12E-15 Yes chr6-26381629-2
NM_003543 HIST1H4H chr6:26393535-26393476 A_23_P323685 4.03 1.13E-21 3.97 2.14E-21   
NM_021058 HIST1H2BJ chr6:27208356-27208297 A_24_P55148 3.81 3.69E-20 3.81 3.41E-20   
NM_021064 HIST1H2AG chr6:27209136-27209195 A_24_P303354 1.30 2.26E-10 1.08 3.92E-08   chr6-27209294-1
ch6-27210796-2
chr6-272111049-7
BC0166776 HIST1H2AG chr6:27210269-27210328 A_24_P414658 4.19 9.07E-25 4.05 4.31E-24   
NM_003495 HIST1H4I chr6:27215204-27215263 A_24_P20873 1.75 1.69E-06 2.63 4.38E-11   
NM_080593 HIST1H2BK chr6:27221956-27221897 A_23_P145238 2.96 4.33E-10 3.34 1.12E-11 Yes  
NM_080596 HIST1H2AH chr6:27223225-27223284 A_23_P81859 1.67 1.41E-12 1.51 3.81E-11   
NM_003519 HIST1H2BL chr6:27883324-27883265 A_23_P8013 3.25 1.72E-14 3.10 8.91E-14   chr6-27883235-1
NM_003536 HIST1H3H chr6:27886003-27886062 A_23_P333484 4.52 3.48E-25 4.05 4.51E-23 Yes  
NM_021066 HIST1H2AJ/7
HIST1H2AI
chr6:27890225-27890166 A_23_P168014 2.30 6.42E-10 2.11 6.71E-09   chr6-27890034-2
NM_021066 HIST1H2AJ/
HIST1H2AI
chr6:27890432-27890373 A_24_P394510 2.44 5.52E-08 2.34 1.62E-07   
NM_003521 HIST1H2BM chr6:27890982-27891041 A_24_P3783 3.29 2.61E-14 3.39 8.13E-15   
NM_003510 HIST1H2AK chr6:27913767-27913708 A_24_P217848 1.56 1.98E-13 1.48 1.27E-12   
NM_003520 HIST1H2BN8 chr6:27914524-27914583 A_23_P402081 3.46 6.89E-19 3.45 7.27E-19   chr6-27927954-1
NM_003511 HIST1H2AL chr6:27941481-27941540 A_23_P363174 1.73 2.13E-11 1.97 2.31E-13   chr6-27941554-1
NM_005322 HIST1H1B chr6:27942667-27942608 A_23_P250385 -1.35 8.17E-03 -1.61 2.22E-03   
NM_003546 HIST1H4L chr6:27948987-27948928 A_23_P70480 -1.46 3.81E-02 -1.59 3.28E-02   
NM_003514 HIST1H2AM chr6:27968545-27968486 A_32_P221799 4.10 3.17E-22 3.58 8.93E-20   
NM_003514 HIST1H2AM chr6:27968615-27968556 A_24_P86389 2.40 5.41E-15 2.35 1.10E-14   
NM_003527 HIST1H2BO chr6:27969567-27969626 A_23_P59069 3.25 1.97E-17 3.23 2.20E-17   
9BC020884 HIST4H4 chr12:14813388-14813329 A_24_P261691 1.14 9.21E-09 1.68 5.34E-14   
NM_002105 H2AFX chr11:118469860-118469801 A_24_P38895 0.92 8.28E-06 0.82 6.13E-05   
NM_177925 H2AFJ chr12:14818894-14818953 A_24_P236003 1.08 1.95E-12 0.91 4.53E-10   
NM_177925 H2AFJ chr12:14819082-14819141 A_23_P204277 0.69 3.92E-06 0.80 1.51E-07   
  1. 1Both scores of 106/111 bits, 2HIST2H2BC - score of 100/111 bits, 3Also aligns to NM_138720: HIST1H2BD transcript variant 2, includes polyA, 4HIST1H3D - score of 104/111 bits, 5BC012185/HIST1H3G cDNA clone IMAGE:4563941, includes polyA, 6BC016677/HIST1H2AG cDNA clone IMAGE 4342191, includes poly,7Both scores of 110/111 bits, 8HIST1H2BL, HIST1H2BK, HIST2H2BF, HIST2H2BF, HIST1H2BI, score of 106 to 100 bits, 9BC020884/HIST4H4 cDNA clone IMAGE:4619662, includes polyA, * annotated as HIST2HAA, #Genome location-read count