Gene expression analysis
Analysis of gene expression of the TSC22D domain family in AML cell lines
Cancer Cell Line Encyclopedia (CCLE) is a multiomics online database collection of 1378 cell lines[9]. The expression data of TSC22D domain family genes in forty-four AML cell lines was downloaded from Expression 21Q4 Public dataset in the CCLE database (Supplementary Material 2) and then used by the cluster heatmap tool from the website (http://www.bioinformatics.com.cn) for visualization.
EMBL-EBI is an integrated bioinformatics research database[10].The data and figures related to gene expression of the TSC22D domain family in fourteen AML cell lines were downloaded from Expression Atlas dataset in the EMBL-EBI database (Supplementary Material 3).
Human Protein Atlas (HPA) is a comprehensive database of proteomics, transcriptomics, and systems biology data[11]. The pictures of gene expression of the TSC22D domain family in five AML cell lines were downloaded from the HPA database.
Analysis of gene expression of the TSC22D domain family in AML cells and normal hematopoietic stem cells
Oncomine is the world's largest database of oncogene chips and integrated data mining platforms [12]. Data of gene expression of the TSC22D domain family in AML cells and CD34-positive peripheral blood cells was downloaded from the Valk leukemia dataset[13] in the Oncomine database and then used by GraphPad Prism 8 for statistical analysis (Supplementary Material 4).
BloodSpot is an online open data platform with data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases that provides gene expression profiles and gene traits in healthy and malignant hematopoiesis, as well as Kaplan–Meier survival maps[14] . Data of gene expression of the TSC22D domain family in AML cells and normal hematopoietic stem cells was downloaded from the normal hematopoiesis with AML dataset (Supplementary Material 5) and the blood- pool AML samples with normal cells dataset (Supplementary Material 6) in the BloodSpot database. Then the expression data was used by GraphPad Prism 8 for statistical analysis.
Analysis of gene expression of the TSC22D domain family in AML group and normal control group
The expression pictures of the TSC22D domain family genes in AML tissues and healthy bone marrow were downloaded from the Valk leukemia dataset in the Oncomine database.
GEPIA2 is an updated and enhanced online publicly accessible database based on TCGA and Genotype-Tissue Expression (GTEx) databases for tumor and normal samples for gene expression analysis[15] .The pictures of gene expression of the TSC22D domain family in AML tissues and normal tissues were downloaded from the GEPIA2 database.
Data of the TSC22D domain family genes in AML tissues and healthy bone marrow samples was downloaded from the Leukemia MILE Study dataset (GSE13159) in the BloodSpot database (Supplementary Material 7) and used by GraphPad Prism 8 for statistical analysis.
Survival analysis
UALCAN is an online, accessible, and interactive network resource for cancer omics data analysis[16] .
GSCALite is an open, online, web-based platform for genomic cancer analysis[17].
The pictures of the effect of the TSC22D domain family gene expression on AML patient survival were downloaded from the GEPIA2, UALCAN, BloodSpot, and GSCALite databases.
Genetic alteration and copy number variation (CNV) analysis of TSC22D3
cBioPortal is a public database to interactively explore multidimensional genomic datasets of cancers[18]. The figures related to the genetic alterations and the survival data of AML patients grouped according to TSC22D3 expression were downloaded from the TCGA PanCancer dataset in the cBioPortal database.
The pictures of the CNV summary and survival analysis of TSC22D3 in AML were downloaded from the GSCALite database.
Functional enrichment analysis of TSC22D3
TRRUST Version 2 is an online, open database of human and mouse transcriptional regulatory networks[19] .
The gene ontology biological process, disease ontology, and KEGG pathway data associated with human TSC22D3 transcription factor (TF) were downloaded from TRRUST Version 2 (Supplementary Material 8) and then used by the bar with a color gredient tool from the website(http://www.bioinformatics.com.cn) for visualization.
Protein–protein interaction (PPI) analysis of TSC22D3
AnimalTFDB3.0 is an online database aimed at providing the most comprehensive and accurate information for animal (including human) TFs and cofactors[20].
STRING is an online open database aimed at providing customized protein–protein networks[21] .
The pictures of the PPI analysis of TSC22D3 were downloaded from the AnimalTFDB3.0 and STRING database.
Harmonizome is an online database of processed datasets of gene and protein knowledge from more than 70 major online sources[22]. Data of PPI analysis of TSC22D3 was downloaded from the Harmonizome database (Supplementary Material 9) and then used by Cytoscape[23] analysis software to visualize the results.
Analysis of TSC22D3 regulated kinases
Data of the predicted TSC22D3 kinase interactions was downloaded from the Harmonizome database (Supplementary Material 10) and used by the circular heatmap tool from the website (http://www.bioinformatics.com.cn) for visualization.
Analysis of TSC22D3 regulated miRNAs
TargetScanHuman 8.0 is an online database that predicts relationships between human miRNAs and target genes[24]. Data of the conserved miRNA families of TSC22D3 was downloaded from the TargetScanHuman 8.0 database (Supplementary Material 11) and then used by the flower plot tool from the website (http://www.bioinformatics.com.cn) for visualization.
MiRDB is an online database for the prediction of miRNA target genes[25] .
Data of the predicted miRNAs of TSC22D3 was downloaded from the miRDB database (Supplementary Material 12) and then used by the flower plot tool from the website (http://www.bioinformatics.com.cn) for visualization.
The Encyclopedia of RNA Interactomes (ENCORI) is an online open source platform for studying data on RNA interactions[26] .
Data of the predicted miRNAs of TSC22D3 was downloaded from the ENCORI database (Supplementary Material 13) and used by Cytoscape analysis software to visualize the results.
Immune infiltration analysis of TSC22D3
Data of the correlation between the TSC22D3 expression and immune infiltration in AML wasdownloaded from the GSCALite database (Supplementary Material 14) and used by the correlation coefficient analysis tool from the website (http://www.bioinformatics.com.cn) for visualization.
GEPIA2021 is an online database for tumor immune invasion analysis[27].The CIBERSORT algorithm was used to explore the correlation between TSC22D3 expression and immune infiltration in AML.