Splicing Factor Regulation

Gene co-expression module in Macrophages

View this module in SCUBA

Why this annotation

Hub genes include TRA2B (transformer-2 beta, splicing regulator), WSB1 (WD repeat and SOCS box protein, ubiquitin ligase adaptor/hypoxia response), CCNL1 (cyclin L1, involved in splicing regulation), MCL1 (anti-apoptotic BCL-2 family, survival), PCF11 (cleavage/polyadenylation factor), FAM53C, PPP1R10 (protein phosphatase 1 regulatory subunit), INPPL1 (SHIP2, phosphoinositide phosphatase), IFRD1 (interferon-related developmental regulator), CLK1 (CDC-like kinase, phosphorylates SR splicing factors), CELF1 (RNA-binding/splicing), NAMPT (nicotinamide phosphoribosyltransferase, NAD biosynthesis, inflammatory mediator), MAT2A (methionine adenosyltransferase, one-carbon metabolism), SLC33A1 (acetyl-CoA transporter). The module combines splicing regulators (TRA2B, CCNL1, CLK1, CELF1, PCF11) with survival/metabolic genes (MCL1, NAMPT, MAT2A). NAMPT is notably enriched in mono_mac (3.4x) and is a key metabolic/inflammatory mediator. The splicing-regulatory theme (TRA2B, CLK1, CCNL1, CELF1) connects this module to neighbors M88, M56, M67. MCL1 and NAMPT add a survival/metabolic layer. The best label captures the splicing kinase/regulation aspect with survival signaling.

Genes

ARAP1, CCNL1, CELF1, CLK1, FAM53C, IFRD1, INPPL1, KIDINS220, MAN2C1, MAT2A, MCL1, NABP1, NAMPT, NXF1, PCF11, PPP1R10, SECISBP2, SLC33A1, TOB2, TRA2B, WSB1

Most correlated modules

• Chromatin Transcriptional Regulation · correlation 0.96
• RNA Splicing Processing · correlation 0.94
• General Cellular Maintenance · correlation 0.94
• Pre-mRNA Splicing · correlation 0.94
• Anti-inflammatory Response · correlation 0.94
• Mixed Regulatory Signaling · correlation 0.94
• Pre-mRNA Splicing · correlation 0.94
• Chromatin Regulatory Genes · correlation 0.93

Module annotations were drafted by a large language model from the module's genes, then reviewed and approved by a domain expert. See sources & licences.