Rename hyperdiploid to high hyperdiploid

Molmed · Oct 11, 2024 · cb1e2c7 · cb1e2c7
1 parent 8994d69
commit cb1e2c7
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Showing 5 changed files with 203 additions and 204 deletions.
diff --git a/conf/subtypes.yml b/conf/subtypes.yml
@@ -1,6 +1,6 @@
 base: &base
   aneuploidy:
-    - hyperdiploid
+    - high hyperdiploid
     - low hyperdiploid
     - iAMP21
   ph-group:
@@ -29,11 +29,10 @@ base: &base
     - NUTM1-r
   Control:
     - Control
-
 dnam:
   <<: *base
   aneuploidy:
-    - hyperdiploid
+    - high hyperdiploid
     - low hyperdiploid
     - iAMP21
     - hypodiploid
diff --git a/data/signatures/signature_cpgs_v3.csv b/data/signatures/signature_cpgs_v3.csv
@@ -15,40 +15,40 @@ aneuploidy,14.5,cg22787468,0.0035416452499653778,0.9617316784506511,0.9614220416
 aneuploidy,14.5,cg23715732,0.0004908724704964784,0.9617316784506511,0.9614220416217418,0.9617541156175394,17.0,RPTOR;RPTOR, RPTOR
 aneuploidy,14.5,cg24467190,0.0009690699532818086,0.9617316784506511,0.9614220416217418,0.9617541156175394,2.0,DNAJB2;DNAJB2, DNAJB2
 aneuploidy,14.5,cg24968629,0.0032293394475320864,0.9617316784506511,0.9614220416217418,0.9617541156175394,22.0,CELSR1, CELSR1
-hyperdiploid,4.0,cg01791669,0.0006933870801414055,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,SSH1;SSH1;SSH1, SSH1
-hyperdiploid,4.0,cg02696971,0.0005063440118138447,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,CBLB, CBLB
-hyperdiploid,4.0,cg02846963,0.0016218278469571766,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,NA,
-hyperdiploid,4.0,cg03001048,0.0011067685000126835,0.9844372677935618,0.9821678898565079,0.9852845664177959,1.0,NOS1AP;NOS1AP, NOS1AP
-hyperdiploid,4.0,cg03976877,0.001559897828863304,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,VIPR2;VIPR2, VIPR2
-hyperdiploid,4.0,cg04970438,0.0005839686710663772,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,TAF3, TAF3
-hyperdiploid,4.0,cg05184729,0.0006880496500216584,0.9844372677935618,0.9821678898565079,0.9852845664177959,5.0,NA,
-hyperdiploid,4.0,cg06834427,0.0008560436678741736,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NA,
-hyperdiploid,4.0,cg07543883,0.0004591176505960928,0.9844372677935618,0.9821678898565079,0.9852845664177959,19.0,ANGPTL6;ANGPTL6, ANGPTL6
-hyperdiploid,4.0,cg08202165,0.0011356967583671107,0.9844372677935618,0.9821678898565079,0.9852845664177959,6.0,NA,
-hyperdiploid,4.0,cg08376828,0.000863090676883757,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,NA,
-hyperdiploid,4.0,cg08882216,0.001445133815026023,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,EPHB6, EPHB6
-hyperdiploid,4.0,cg09719124,0.0007201004771551343,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,LMCD1, LMCD1
-hyperdiploid,4.0,cg09894698,0.0006092814319926413,0.9844372677935618,0.9821678898565079,0.9852845664177959,11.0,ASCL2, ASCL2
-hyperdiploid,4.0,cg10063047,0.0009468274925516919,0.9844372677935618,0.9821678898565079,0.9852845664177959,21.0,FTCD;FTCD, FTCD
-hyperdiploid,4.0,cg10206933,0.001218846081311591,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,BNIP3, BNIP3
-hyperdiploid,4.0,cg10362869,0.0005226053639846602,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NCKAP5;NCKAP5, NCKAP5
-hyperdiploid,4.0,cg10619342,0.001171910087945308,0.9844372677935618,0.9821678898565079,0.9852845664177959,15.0,LOC390594, LOC390594
-hyperdiploid,4.0,cg11189837,0.0007595868220523441,0.9844372677935618,0.9821678898565079,0.9852845664177959,21.0,ADAMTS1, ADAMTS1
-hyperdiploid,4.0,cg11199770,0.002369956189339993,0.9844372677935618,0.9821678898565079,0.9852845664177959,19.0,TSHZ3, TSHZ3
-hyperdiploid,4.0,cg13794530,0.0008076628352490202,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,VIPR2;VIPR2, VIPR2
-hyperdiploid,4.0,cg15057852,0.00038785328278000277,0.9844372677935618,0.9821678898565079,0.9852845664177959,20.0,KIF16B, KIF16B
-hyperdiploid,4.0,cg16200531,0.0009490587015759679,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NA,
-hyperdiploid,4.0,cg17090401,0.0004038314176245101,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,FAT1, FAT1
-hyperdiploid,4.0,cg17716765,0.002846892887401596,0.9844372677935618,0.9821678898565079,0.9852845664177959,15.0,APBA2;APBA2, APBA2
-hyperdiploid,4.0,cg20663432,0.0016308789793530857,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,ANO2, ANO2
-hyperdiploid,4.0,cg20719675,0.0004429979070884313,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,CHRNA1;CHRNA1, CHRNA1
-hyperdiploid,4.0,cg23320499,0.0016139095838665,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,DUSP16, DUSP16
-hyperdiploid,4.0,cg23584087,0.0019535452447866724,0.9844372677935618,0.9821678898565079,0.9852845664177959,13.0,KL, KL
-hyperdiploid,4.0,cg25857569,0.0010910210025555317,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,PPM1L, PPM1L
-hyperdiploid,4.0,cg26071526,0.0021039922435095292,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,TACC2;TACC2;TACC2;TACC2;TACC2;TACC2, TACC2
-hyperdiploid,4.0,cg26282731,0.0019345048216024875,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,ARHGAP10, ARHGAP10
-hyperdiploid,4.0,cg26645082,0.0009572601819929528,0.9844372677935618,0.9821678898565079,0.9852845664177959,11.0,SHANK2, SHANK2
-hyperdiploid,4.0,cg27180671,0.0012327209124322126,0.9844372677935618,0.9821678898565079,0.9852845664177959,17.0,PITPNC1;PITPNC1, PITPNC1
+high hyperdiploid,4.0,cg01791669,0.0006933870801414055,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,SSH1;SSH1;SSH1, SSH1
+high hyperdiploid,4.0,cg02696971,0.0005063440118138447,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,CBLB, CBLB
+high hyperdiploid,4.0,cg02846963,0.0016218278469571766,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,NA,
+high hyperdiploid,4.0,cg03001048,0.0011067685000126835,0.9844372677935618,0.9821678898565079,0.9852845664177959,1.0,NOS1AP;NOS1AP, NOS1AP
+high hyperdiploid,4.0,cg03976877,0.001559897828863304,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,VIPR2;VIPR2, VIPR2
+high hyperdiploid,4.0,cg04970438,0.0005839686710663772,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,TAF3, TAF3
+high hyperdiploid,4.0,cg05184729,0.0006880496500216584,0.9844372677935618,0.9821678898565079,0.9852845664177959,5.0,NA,
+high hyperdiploid,4.0,cg06834427,0.0008560436678741736,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NA,
+high hyperdiploid,4.0,cg07543883,0.0004591176505960928,0.9844372677935618,0.9821678898565079,0.9852845664177959,19.0,ANGPTL6;ANGPTL6, ANGPTL6
+high hyperdiploid,4.0,cg08202165,0.0011356967583671107,0.9844372677935618,0.9821678898565079,0.9852845664177959,6.0,NA,
+high hyperdiploid,4.0,cg08376828,0.000863090676883757,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,NA,
+high hyperdiploid,4.0,cg08882216,0.001445133815026023,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,EPHB6, EPHB6
+high hyperdiploid,4.0,cg09719124,0.0007201004771551343,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,LMCD1, LMCD1
+high hyperdiploid,4.0,cg09894698,0.0006092814319926413,0.9844372677935618,0.9821678898565079,0.9852845664177959,11.0,ASCL2, ASCL2
+high hyperdiploid,4.0,cg10063047,0.0009468274925516919,0.9844372677935618,0.9821678898565079,0.9852845664177959,21.0,FTCD;FTCD, FTCD
+high hyperdiploid,4.0,cg10206933,0.001218846081311591,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,BNIP3, BNIP3
+high hyperdiploid,4.0,cg10362869,0.0005226053639846602,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NCKAP5;NCKAP5, NCKAP5
+high hyperdiploid,4.0,cg10619342,0.001171910087945308,0.9844372677935618,0.9821678898565079,0.9852845664177959,15.0,LOC390594, LOC390594
+high hyperdiploid,4.0,cg11189837,0.0007595868220523441,0.9844372677935618,0.9821678898565079,0.9852845664177959,21.0,ADAMTS1, ADAMTS1
+high hyperdiploid,4.0,cg11199770,0.002369956189339993,0.9844372677935618,0.9821678898565079,0.9852845664177959,19.0,TSHZ3, TSHZ3
+high hyperdiploid,4.0,cg13794530,0.0008076628352490202,0.9844372677935618,0.9821678898565079,0.9852845664177959,7.0,VIPR2;VIPR2, VIPR2
+high hyperdiploid,4.0,cg15057852,0.00038785328278000277,0.9844372677935618,0.9821678898565079,0.9852845664177959,20.0,KIF16B, KIF16B
+high hyperdiploid,4.0,cg16200531,0.0009490587015759679,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,NA,
+high hyperdiploid,4.0,cg17090401,0.0004038314176245101,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,FAT1, FAT1
+high hyperdiploid,4.0,cg17716765,0.002846892887401596,0.9844372677935618,0.9821678898565079,0.9852845664177959,15.0,APBA2;APBA2, APBA2
+high hyperdiploid,4.0,cg20663432,0.0016308789793530857,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,ANO2, ANO2
+high hyperdiploid,4.0,cg20719675,0.0004429979070884313,0.9844372677935618,0.9821678898565079,0.9852845664177959,2.0,CHRNA1;CHRNA1, CHRNA1
+high hyperdiploid,4.0,cg23320499,0.0016139095838665,0.9844372677935618,0.9821678898565079,0.9852845664177959,12.0,DUSP16, DUSP16
+high hyperdiploid,4.0,cg23584087,0.0019535452447866724,0.9844372677935618,0.9821678898565079,0.9852845664177959,13.0,KL, KL
+high hyperdiploid,4.0,cg25857569,0.0010910210025555317,0.9844372677935618,0.9821678898565079,0.9852845664177959,3.0,PPM1L, PPM1L
+high hyperdiploid,4.0,cg26071526,0.0021039922435095292,0.9844372677935618,0.9821678898565079,0.9852845664177959,10.0,TACC2;TACC2;TACC2;TACC2;TACC2;TACC2, TACC2
+high hyperdiploid,4.0,cg26282731,0.0019345048216024875,0.9844372677935618,0.9821678898565079,0.9852845664177959,4.0,ARHGAP10, ARHGAP10
+high hyperdiploid,4.0,cg26645082,0.0009572601819929528,0.9844372677935618,0.9821678898565079,0.9852845664177959,11.0,SHANK2, SHANK2
+high hyperdiploid,4.0,cg27180671,0.0012327209124322126,0.9844372677935618,0.9821678898565079,0.9852845664177959,17.0,PITPNC1;PITPNC1, PITPNC1
 low hyperdiploid,2.5,cg01154505,9.455060155697214e-05,0.9915208775654637,0.9917459636767609,0.991105173693409,2.0,FBLN7;FBLN7, FBLN7
 low hyperdiploid,2.5,cg02068356,0.0002994102382637451,0.9915208775654637,0.9917459636767609,0.991105173693409,1.0,NA,
 low hyperdiploid,2.5,cg02610360,0.0016338162854547388,0.9915208775654637,0.9917459636767609,0.991105173693409,11.0,TMEM136, TMEM136

diff --git a/data/signatures/signature_genes_v3.csv b/data/signatures/signature_genes_v3.csv
@@ -28,34 +28,34 @@ aneuploidy,5.0,ENSG00000205755,0.0025031964905207105,0.977088736104192,0.9759283
 aneuploidy,5.0,ENSG00000213416,0.0017475780730277766,0.977088736104192,0.9759283074382226,0.9760419496930308,KRTAP4-12,17
 aneuploidy,5.0,ENSG00000267206,0.0004019097167064514,0.977088736104192,0.9759283074382226,0.9760419496930308,LCN6,9
 aneuploidy,5.0,ENSG00000274443,0.0008024923887781239,0.977088736104192,0.9759283074382226,0.9760419496930308,C8orf89,8
-hyperdiploidy,3.0,ENSG00000057019,0.0011226551226551252,1.0,0.9952955044955044,0.9965021645021644,DCBLD2,3
-hyperdiploidy,3.0,ENSG00000095585,0.0004939682539682551,1.0,0.9952955044955044,0.9965021645021644,BLNK,10
-hyperdiploidy,3.0,ENSG00000110077,0.0007634054834054851,1.0,0.9952955044955044,0.9965021645021644,MS4A6A,11
-hyperdiploidy,3.0,ENSG00000115457,0.013471861471861501,1.0,0.9952955044955044,0.9965021645021644,IGFBP2,2
-hyperdiploidy,3.0,ENSG00000124491,0.006991364764268001,1.0,0.9952955044955044,0.9965021645021644,F13A1,6
-hyperdiploidy,3.0,ENSG00000132465,0.004217449074223276,1.0,0.9952955044955044,0.9965021645021644,JCHAIN,4
-hyperdiploidy,3.0,ENSG00000133067,0.0015268109668109702,1.0,0.9952955044955044,0.9965021645021644,LGR6,1
-hyperdiploidy,3.0,ENSG00000143036,0.00035924963924964005,1.0,0.9952955044955044,0.9965021645021644,SLC44A3,1
-hyperdiploidy,3.0,ENSG00000145087,0.00044906204906205007,1.0,0.9952955044955044,0.9965021645021644,STXBP5L,3
-hyperdiploidy,3.0,ENSG00000147180,0.009144995506285843,1.0,0.9952955044955044,0.9965021645021644,ZNF711,X
-hyperdiploidy,3.0,ENSG00000164938,0.004442913645494298,1.0,0.9952955044955044,0.9965021645021644,TP53INP1,8
-hyperdiploidy,3.0,ENSG00000166503,0.014460827487924276,1.0,0.9952955044955044,0.9965021645021644,HDGFL3,15
-hyperdiploidy,3.0,ENSG00000168671,0.010982415720480254,1.0,0.9952955044955044,0.9965021645021644,UGT3A2,5
-hyperdiploidy,3.0,ENSG00000170561,0.007409523809523826,1.0,0.9952955044955044,0.9965021645021644,IRX2,5
-hyperdiploidy,3.0,ENSG00000174059,0.0023351226551226604,1.0,0.9952955044955044,0.9965021645021644,CD34,1
-hyperdiploidy,3.0,ENSG00000179862,0.002827223815610918,1.0,0.9952955044955044,0.9965021645021644,CITED4,1
-hyperdiploidy,3.0,ENSG00000182272,0.0025128803812674828,1.0,0.9952955044955044,0.9965021645021644,B4GALNT4,11
-hyperdiploidy,3.0,ENSG00000196653,0.007903492063492081,1.0,0.9952955044955044,0.9965021645021644,ZNF502,3
-hyperdiploidy,3.0,ENSG00000283977,0.0006286868686868701,1.0,0.9952955044955044,0.9965021645021644,AC084337.2,11
-low hyperdiploidy,2.5,ENSG00000147183,0.0007412924424972647,1.0,0.9673202614379086,0.9731601731601731,CPXCR1,X
-low hyperdiploidy,2.5,ENSG00000167768,0.0007824753559693349,1.0,0.9673202614379086,0.9731601731601731,KRT1,12
-low hyperdiploidy,2.5,ENSG00000171643,0.0005353778751369134,1.0,0.9673202614379086,0.9731601731601731,S100Z,5
-low hyperdiploidy,2.5,ENSG00000198157,0.0005353778751369134,1.0,0.9673202614379086,0.9731601731601731,HMGN5,X
-low hyperdiploidy,2.5,ENSG00000235272,0.0007824753559693349,1.0,0.9673202614379086,0.9731601731601731,RAMACL,6
-low hyperdiploidy,2.5,ENSG00000265118,0.004035925520262885,1.0,0.9673202614379086,0.9731601731601731,AC134669.1,17
-low hyperdiploidy,2.5,ENSG00000266076,0.0017708652792990211,1.0,0.9673202614379086,0.9731601731601731,AC004805.1,17
-low hyperdiploidy,2.5,ENSG00000269897,0.005271412924424993,1.0,0.9673202614379086,0.9731601731601731,COMMD3-BMI1,10
-low hyperdiploidy,2.5,ENSG00000285283,0.0011531215772179672,1.0,0.9673202614379086,0.9731601731601731,AL035078.4,11
+high hyperdiploid,3.0,ENSG00000057019,0.0011226551226551252,1.0,0.9952955044955044,0.9965021645021644,DCBLD2,3
+high hyperdiploid,3.0,ENSG00000095585,0.0004939682539682551,1.0,0.9952955044955044,0.9965021645021644,BLNK,10
+high hyperdiploid,3.0,ENSG00000110077,0.0007634054834054851,1.0,0.9952955044955044,0.9965021645021644,MS4A6A,11
+high hyperdiploid,3.0,ENSG00000115457,0.013471861471861501,1.0,0.9952955044955044,0.9965021645021644,IGFBP2,2
+high hyperdiploid,3.0,ENSG00000124491,0.006991364764268001,1.0,0.9952955044955044,0.9965021645021644,F13A1,6
+high hyperdiploid,3.0,ENSG00000132465,0.004217449074223276,1.0,0.9952955044955044,0.9965021645021644,JCHAIN,4
+high hyperdiploid,3.0,ENSG00000133067,0.0015268109668109702,1.0,0.9952955044955044,0.9965021645021644,LGR6,1
+high hyperdiploid,3.0,ENSG00000143036,0.00035924963924964005,1.0,0.9952955044955044,0.9965021645021644,SLC44A3,1
+high hyperdiploid,3.0,ENSG00000145087,0.00044906204906205007,1.0,0.9952955044955044,0.9965021645021644,STXBP5L,3
+high hyperdiploid,3.0,ENSG00000147180,0.009144995506285843,1.0,0.9952955044955044,0.9965021645021644,ZNF711,X
+high hyperdiploid,3.0,ENSG00000164938,0.004442913645494298,1.0,0.9952955044955044,0.9965021645021644,TP53INP1,8
+high hyperdiploid,3.0,ENSG00000166503,0.014460827487924276,1.0,0.9952955044955044,0.9965021645021644,HDGFL3,15
+high hyperdiploid,3.0,ENSG00000168671,0.010982415720480254,1.0,0.9952955044955044,0.9965021645021644,UGT3A2,5
+high hyperdiploid,3.0,ENSG00000170561,0.007409523809523826,1.0,0.9952955044955044,0.9965021645021644,IRX2,5
+high hyperdiploid,3.0,ENSG00000174059,0.0023351226551226604,1.0,0.9952955044955044,0.9965021645021644,CD34,1
+high hyperdiploid,3.0,ENSG00000179862,0.002827223815610918,1.0,0.9952955044955044,0.9965021645021644,CITED4,1
+high hyperdiploid,3.0,ENSG00000182272,0.0025128803812674828,1.0,0.9952955044955044,0.9965021645021644,B4GALNT4,11
+high hyperdiploid,3.0,ENSG00000196653,0.007903492063492081,1.0,0.9952955044955044,0.9965021645021644,ZNF502,3
+high hyperdiploid,3.0,ENSG00000283977,0.0006286868686868701,1.0,0.9952955044955044,0.9965021645021644,AC084337.2,11
+low hyperdiploid,2.5,ENSG00000147183,0.0007412924424972647,1.0,0.9673202614379086,0.9731601731601731,CPXCR1,X
+low hyperdiploid,2.5,ENSG00000167768,0.0007824753559693349,1.0,0.9673202614379086,0.9731601731601731,KRT1,12
+low hyperdiploid,2.5,ENSG00000171643,0.0005353778751369134,1.0,0.9673202614379086,0.9731601731601731,S100Z,5
+low hyperdiploid,2.5,ENSG00000198157,0.0005353778751369134,1.0,0.9673202614379086,0.9731601731601731,HMGN5,X
+low hyperdiploid,2.5,ENSG00000235272,0.0007824753559693349,1.0,0.9673202614379086,0.9731601731601731,RAMACL,6
+low hyperdiploid,2.5,ENSG00000265118,0.004035925520262885,1.0,0.9673202614379086,0.9731601731601731,AC134669.1,17
+low hyperdiploid,2.5,ENSG00000266076,0.0017708652792990211,1.0,0.9673202614379086,0.9731601731601731,AC004805.1,17
+low hyperdiploid,2.5,ENSG00000269897,0.005271412924424993,1.0,0.9673202614379086,0.9731601731601731,COMMD3-BMI1,10
+low hyperdiploid,2.5,ENSG00000285283,0.0011531215772179672,1.0,0.9673202614379086,0.9731601731601731,AL035078.4,11
 iAMP21,2.8,ENSG00000022556,0.005127931769722824,1.0,0.9939202841602841,0.9961069518716578,NLRP2,19
 iAMP21,2.8,ENSG00000101493,0.020234541577825203,1.0,0.9939202841602841,0.9961069518716578,ZNF516,18
 iAMP21,2.8,ENSG00000105642,0.019911158493248083,1.0,0.9939202841602841,0.9961069518716578,KCNN1,19