Extended Data Table 3 |.
Comparison between disclosed hits in a previous study and in this work
| gene | GRCh38 | Splice Junction Found | baseMean | log2FoldChange | IfcSE | stat | pvalue | padj |
|---|---|---|---|---|---|---|---|---|
| ABHD10 | chr3:111990700–111990751 | 3:111987052–111990699 | 9.809816136 | 0.614834912 | 0.466585174 | 1.317733495 | 0.187592878 | 0.999998084 |
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| ||||||||
| ADAM12 | chr10:126041344–126042235 | Not Found | ||||||
|
| ||||||||
| AKT1 | chr14:104793127–104793127 | 14:104792723–104793126 | 41.80684788 | −0.26101857 | 0.231973571 | −1.125208222 | 0.26050081 | 0.999998084 |
|
| ||||||||
| ANXA11 | chr10:80180941–80181136 | 10:80176156–80180940 | 10.82449812 | −0.218718834 | 0.42387425 | −0.515999343 | 0.605854868 | 0.999998084 |
|
| ||||||||
| APLP2 | chr11:130123612–130123779 | 11:130122514–130123611 | 490.449954 | 0.356584851 | 0.084290488 | 4.230428123 | 2.33E-05 | 0.007262767 |
|
| ||||||||
| APPL2 | chr12:105233091–105233405 | Not Found | ||||||
|
| ||||||||
| ARMCX6 | chrX:101617283–101617370 | X:101616767–101617282 | 1.554115827 | 4.038853198 | 1.327731995 | 3.041919011 | 0.002350751 | 0.067486942 |
| X:101616767–101617291 | 1.979014083 | 4.34277536 | 1.312975149 | 3.307583822 | 0.000941045 | 0.043636072 | ||
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| ||||||||
| ATG5 | chr6:106308364–106308491 | 6:106293107–106308363 | 172.1443391 | −0.141439917 | 0.116742213 | −1.211557606 | 0.225681771 | 0.999998084 |
|
| ||||||||
| AXIN1 | chr16:291190–291297 | 16:289608–291189 | 12.88615371 | 0.567337279 | 0.398949658 | 1.422077369 | 0.155003792 | 0.986220545 |
|
| ||||||||
| BAIAP2 | chr17:81110914–81110959 | 17:81108510–81110913 | 4.125817311 | 1.37672654 | 0.718313789 | 1.916608815 | 0.055287647 | 0.636240125 |
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| ||||||||
| CCNB1IP1 | chr14:20317794–20317974 | Not Found | ||||||
|
| ||||||||
| CCT7 | chr2:73235550–73235645 | 2:73234385–73235549 | 5.106947198 | 1.017231089 | 0.677438559 | 1.501584277 | 0.133204506 | 0.949522936 |
|
| ||||||||
| CEP57 | chr11:95795516–95795559 | 11:95790744–95795515 | 14.58205551 | −0.09994828 | 0.374087616 | −0.267178799 | 0.789331499 | 0.999998084 |
|
| ||||||||
| CSF1 | chr1:109926063–109926743 | 1:109925203–109926062 | 0.512925465 | −2.527906075 | 1.798973282 | −1.405193785 | 0.159963662 | NA |
|
| ||||||||
| DLGAP4 | chr20:36499242–36499321 | 20:36497067–36499241 | 2.321757283 | 4.629312735 | 1.234758303 | 3.7491651 | 0.000177424 | 0.019705473 |
|
| ||||||||
| EPN1 | chr19:55676625–55677218 | 19:55677219–55677549 | 6.792614573 | 0.137794309 | 0.548684186 | 0.251135923 | 0.801709023 | 0.999998084 |
| EPN1 | chr19:55677550–55677734 | Not Found | ||||||
|
| ||||||||
| ERGIC3 | chr20:35554372–35554386 | 20:35548866–35554371 | 28.83410289 | 4.036660975 | 0.450049004 | 8.969380978 | 2.98E-19 | 1.36E-14 |
| 20:35549208–35554371 | 1.211236736 | 3.671748012 | 1.402133721 | 2.618686047 | 0.008826914 | NA | ||
|
| ||||||||
| FOXM1 | chr12:2861299–2861412 | 12:2859664–2861298 | 10.02538278 | 1.393165926 | 0.478256758 | 2.913008346 | 0.00357965 | 0.083406816 |
|
| ||||||||
| GGCT | chr7:30497741–30497896 | Not Found | ||||||
|
| ||||||||
| GRAMD3 | chr5:126466294–126466336 | 5:119456369–119471635 | 11.26191388 | 0.47467429 | 0.423301943 | 1.121360999 | 0.26213423 | 0.999998084 |
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| ||||||||
| HSD17B4 | chr5:119471636–119471700 | 5:119457369–119471635 | 0.494108183 | 2.368999879 | 1.817387698 | 1.303519267 | 0.192397543 | NA |
|
| ||||||||
| LARP7 | chr4:112637644–112637787 | 4:112637240–112637643 | 27.19269642 | 3.451696147 | 0.399919423 | 8.630979006 | 6.08E-18 | 1.58E-13 |
|
| ||||||||
| LARP7 | chr4:112644425–112644488 | 4:112638674–112644424 | 0.728760441 | 2.934691979 | 1.612411811 | 1.820063558 | 0.068749326 | NA |
|
| ||||||||
| LRRC42 | chr1:53947788–53947821 | 1:53946550–53947787 | 29.09604567 | −0.664904577 | 0.265177179 | −2.507397428 | 0.012162388 | 0.190363981 |
|
| ||||||||
| MADD | chr1l:47292543–47292596 | 11:47290817–47292542 | 2.731362466 | 4.872013188 | 1.210216484 | 4.025736926 | 5.68E-05 | 0.011525541 |
|
| ||||||||
| MAN1B1 | chr9:137088268–137088398 | Not Found | ||||||
|
| ||||||||
| MRPL39 | chr21:25587701–25587789 | Not Found | ||||||
|
| ||||||||
| PCBP4 | chr3:51962810–51962892 | 3:51961305–51962809 | 1.182311825 | 3.691518129 | 1.422245816 | 2.595555625 | 0.009443812 | NA |
| 3:51962089–51962809 | 1.216301921 | 3.681908004 | 1.418185239 | 2.59621092 | 0.009425818 | NA | ||
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| ||||||||
| PPHLN1 | chr12:42351885–42352049 | 12:42335975–42351884 | 123.8298057 | −0.046390515 | 0.135503904 | −0.342355562 | 0.732083327 | 0.999998084 |
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| ||||||||
| PRKACB | chr1:84144269–84144548 | 1:111619935–111627469 | 2.568291852 | 1.215471674 | 0.941010031 | 1.291667074 | 0.196472465 | 0.999998084 |
|
| ||||||||
| RAB23 | chr6:57221319–57221459 | Not Found | ||||||
|
| ||||||||
| RAP1A | chr1:111627470–111627563 | Not Found | ||||||
|
| ||||||||
| RCC1 | chr1:28518233–28518308 | Not Found | ||||||
|
| ||||||||
| SREK1 | chr5:66156065–66157740 | 5:66153597–66156064 | 33.02107777 | −0.458074764 | 0.247829652 | −1.848345265 | 0.064552411 | 0.697745988 |
| SREK1 | chr5:66158809–66158932 | 5:66153597–66158808 | 10.54393267 | 0.145262673 | 0.426009401 | 0.340984665 | 0.733115126 | 0.999998084 |
| 5:66158231–66158808 | 7.253095127 | −0.095361539 | 0.528821088 | −0.180328548 | 0.856894645 | 0.999998084 | ||
|
| ||||||||
| STRN3 | chr14:30929201–30929311 | 14:30913658–30929200 | 50.93805874 | 0.932636289 | 0.216274269 | 4.312285011 | 1.62E-05 | 0.005970823 |
| STRN3 | chr14:30918966–30919106 | 14:30919107–30929200 | 46.51202979 | 0.551658841 | 0.208079453 | 2.651193256 | 0.008020793 | 0.130401186 |
| 14:30913658–30918965 | 55.45310576 | 0.329108298 | 0.20344735 | 1.617658317 | 0.105736254 | 0.881349323 | ||
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| ||||||||
| TNRC6A | chr16:24758339–24758360 | 16:24750814–24758338 | 91.74639209 | 0.019177308 | 0.149159372 | 0.128569248 | 0.897698501 | 0.999998084 |
See ref. 8. Column identity from left to right; Column A, Gene ID of genes containing a significantly induced exon as identified by Palacino et al.8; Column B, GRCh38 position of the induced exon; Column C, the associated splice junction of the identified induced exons, if found in our dataset ‘splice junction found’; Columns D–I, Differential expression status of each splice junction in our dataset, DMSO (n = 4) versus 25 nM LMI070 (n = 4). Differential expression was performed using DESeq2. Column D, The mean of normalized counts for all samples ‘baseMean’; Column E, the log2 fold change (maximum likelihood estimate) ‘Log2FoldChange’; Column F, the associated standard error ‘lfcSE’; Column G, the Wald statistic ‘stat’, Column H, the Wald test two-tailed P value ‘p value’; Column I, the Benjamini-Hochberg (BH) multiple testing corrected P value “p adj”. Genes observed to be significant (Padj < 0.05) in our dataset are bolded.