细胞焦亡、铁死亡及铜死亡浅析

自噬(Autophagy) 相关基因：

   Autophagy-associated genes (relevance score > 4) were retrieved at the GeneCards website (https://www.genecards.org/) by searching the term “autophagy.” 

1. A total of 1,287 ARGs were acquired from the Human Autophagy Database (HADb; http://autophagy.lu/clustering/index.html) and Autophagy database (http://autophagy.info/).  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9830320/
2. Human ARGs were downloaded from the HADB website (http://www.autophagy.lu/clustering/index.html, last update time: 2021–12-3), and a total of 206 ARGs were obtained.
3. We extracted 232 autophagy-related genes from the human autophagy database (HADb, http://autophagy.lu/clustering/index.html).
   
   

焦亡(Pyroptosis) 相关基因：

1. We identified 52 pyroptosis-related genes from prior reviews, and they are presented in Table S1 ； https://link.springer.com/article/10.1186/s12885-022-09526-z#Sec2 
2. From Genecards (https://www.genecards.org/), 176 pyroptosis-related genes (PRGs) (Supplementary Table S1) were finally retrieved. https://www.frontiersin.org/articles/10.3389/fgene.2022.1029717/full 
3. We extracted 33 pyroptosis-related genes from prior reviews17,18,19,20, and they are presented in Table S1. https://www.nature.com/articles/s41420-021-00451-x#Sec11 
   

细胞凋亡(Apoptosis) 相关基因：

1. A total of 136 apoptosis-related genes were collected by searching the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database (https://www.kegg.jp/kegg/pathway.html) with the keyword “Apoptosis.” Eventually, 134 apoptosis-related genes were retrieved from the mRNA expression profile of TCGA-LUAD (Supplementary Table S3).  https://www.frontiersin.org/articles/10.3389/fgene.2022.946939/full 
   
2. 87 apoptosis-related genes were recognized within the KEGG_APOPTOSIS gene set from the Molecular Signatures Database (MSigDB, https://www.gsea-msigdb.org/gsea/msigdb). See Supplementary Table S1 for a list of apoptosis-related genes. https://www.frontiersin.org/articles/10.3389/fsurg.2022.863035/full#h6 
3. By reviewing the previous literature, we identified 92 ARGs (Supplementary Table S1).  https://www.frontiersin.org/articles/10.3389/fgene.2022.921163/full#h3
     

铁死亡(Ferroptosis)

1. From the FerrDb database (http://www.zhounan.org/ferrdb/ (accessed on 12 January 2022)), a total of 259 ferroptosis-related genes, including drivers, suppressors, and markers, were collected (Table S1). https://www.mdpi.com/2073-4425/13/6/997  
2. Ferroptosis-related genes were collected from the FerrDb database, and included 108 drivers, 69 suppressors, and 111 markers；https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08296-z
3. A total of 60 ferroptosis genes were identified from prior study (8) (available at https://cdn.amegroups.cn/static/public/atm-22-3736-2.xls). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8908135/ 
4. We have downloaded all ferroptosis-related markers from FerrDb,Citation7 and then retained 246 genes that matched gene signatures in the TCGA-COAD and TCGA-READ data frame (Table S1).  https://www.tandfonline.com/doi/full/10.2147/IJGM.S331378
    

铜死亡（Cuproptosis）相关基因

1.  A total of 13 cuproptosis-related genes (FDX1, LIAS, LIPT1, GCSH, DBT, DLST, DLD, DLAT, PDHA1, PDHB, SLC31A1, ATP7A, and ATP7B) were included for subsequent analysis based on the process of cuproptosis described in the previous study (Tsvetkov et al., 2022). https://www.frontiersin.org/articles/10.3389/fgene.2022.957744/full 
   
2. The list of cuproptosis-related genes (CRGs) refers to the previous literature (14). In the end, ten CRGs were included in our study: FDX1, LIAS, LIPT1, DLD, DLAT, PDHA1, POHB, MTF1, GLS, and CDKN2A.  https://www.frontiersin.org/articles/10.3389/fimmu.2022.998236/full 
   

衰老（SENESCENCE）相关基因

As a measure of cellular senescence, we used an established senescence-related gene set [16] (FRIDMAN.SENESCENCE.UP).  (Additional file 1: Table S1) ;

https://link.springer.com/article/10.1186/s12929-023-00915-5

细胞死亡相关基因

1. 15种：PCD-related genes (PRGs) of these 15 cell death patterns were collated from MSigDB (http://software.broadinstitute.org/gsea/msigdb/index.jsp), Kyoto Encyclopedia of Genes and Genomes, review articles, and manual collection of gene sets from Genecards website (https://www.genecards.org/) [14,15] (Supplementary Table 1) https://www.sciencedirect.com/science/article/pii/S1936523323001705?via%3Dihub#sec0025 

1. 18种：We conducted a literature search [38] and gathered 18 patterns of PCD and key regulatory genes, which included 580 genes related to apoptosis, 367 genes related to autophagy, 7 genes related to alkaliptosis, 338 genes related to anoikis, 19 genes related to cuproptosis, 15 genes related to enteric cell death, 87 genes related to ferroptosis, 34 genes related to immunogenic cell death, 220 genes related to lysosome-dependent cell death, 101 genes related to necroptosis, 8 genes related to netotic cell death, 24 genes related to NETosis, 5 genes related to oxeiptosis, 52 genes related to pyroptosis, 9 genes related to parthanatos, and 66 genes related to paraptosis. Additionally, there were 8 Methuosis genes and 23 Entosis genes, resulting in a total of 1964 PCD-related genes. We removed 416 duplicates, resulting in 1548 PCD-related cluster genes for our analysis (Additional file 9: Table S1) ：参考文献：https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-023-04468-x