Most Variable Genes and Transcription Factors in Acute Lymphoblastic Leukemia Patients

  • Anil Kumar TomarEmail author
  • Rahul Agarwal
  • Bishwajit Kundu
Original research article


Acute lymphoblastic leukemia (ALL) is a hematologic tumor caused by cell cycle aberrations due to accumulating genetic disturbances in the expression of transcription factors (TFs), signaling oncogenes and tumor suppressors. Though survival rate in childhood ALL patients is increased up to 80% with recent medical advances, treatment of adults and childhood relapse cases still remains challenging. Here, we have performed bioinformatics analysis of 207 ALL patients’ mRNA expression data retrieved from the ICGC data portal with an objective to mark out the decisive genes and pathways responsible for ALL pathogenesis and aggression. For analysis, 3361 most variable genes, including 276 transcription factors (out of 16,807 genes) were sorted based on the coefficient of variance. Silhouette width analysis classified 207 ALL patients into 6 subtypes and heat map analysis suggests a need of large and multicenter dataset for non-overlapping subtype classification. Overall, 265 GO terms and 32 KEGG pathways were enriched. The lists were dominated by cancer-associated entries and highlight crucial genes and pathways that can be targeted for designing more specific ALL therapeutics. Differential gene expression analysis identified upregulation of two important genes, JCHAIN and CRLF2 in dead patients’ cohort suggesting their possible involvement in different clinical outcomes in ALL patients undergoing the same treatment.


Gene expression KEGG pathways Leukemia Most variable genes Subtype classification 



This work was supported by grants received by AKT from Science and Engineering Research Board (SERB), Department of Science & Technology, Govt. of India, New Delhi, under National-Postdoctoral Fellowship Scheme (File Number: PDF/2015/000979). Authors also thank the IIT Delhi HPC facility for computational resources.

Compliance with Ethical Standards

Conflict of interest

Authors declare no conflict of interest.

Supplementary material

12539_2019_325_MOESM1_ESM.xlsx (7.9 mb)
Supplementary material 1 (XLSX 8120 KB)


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© International Association of Scientists in the Interdisciplinary Areas 2019

Authors and Affiliations

  1. 1.Kusuma School of Biological SciencesIndian Institute of Technology DelhiNew DelhiIndia
  2. 2.Department of Reproductive BiologyAll India Institute of Medical SciencesNew DelhiIndia

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