MIKA macrophage identity fingerprint genes annotated with M1/M2 gene markers

MIKA (Macrophage Identity Kinetics Archive) is an archive of possible cell state of tissue macrophages across various pathophysiologies. Based on meta-analysis of single-cell RNA-seq datasets, MIKA defines 6 core macrophage identities (S1-S6) that are shared by multiple tissues/ organs (ie. pan-tissue identities), in addition to tissue-specific macrophages. The defining gene fingerprint of each core identity is documented in Li YT. elife. 2025 (https://doi.org/10.7554/eLife.108284.3).

Here, M1/M2 markers, either commonly used or defined by previous studies, are annotated side-by-side to the core identity gene fingerprint. This data table aims to serve as a reference to bridge between M1/M2 markers (often shows ambiguity and mixed character in pathophysiologies) and MIKA identity markers, and should be considered as an extension of Li YT. elife. 2025.

The annotation result shows that the M1/M2 scheme is limited in referencing to a homogenous tissue macrophage cell state as indicated by the MIKA identity.

As shown in the graphs, where common M1/M2 markers are plotted for correlation to each MIKA core identity, some commonly used "M1" or "M2" markers outperform others in labelling macrophages of similar transcriptomic landscape (ie. identity) in tissue-specific manner.

Definition of M1/M2-associated genes follows the gene lists provided by the studies below.
Coates PJ, et al. Cancer Res. 2008 (PMID: 18199539; archived in GSEA)
Oshi M, et al. Sci Rep. 2020 (PMID: 33024179)
*Some genes are flagged as both M1- and M2- associated in this study and are excluded from annotation
*Some genes in this study deviate from common usage (eg. CD163 labelled as an M1 marker)

"Common.marker" is manually annotated, with "M1/2-associated" denoting stronger markers and "M1/2-biased" denoting weaker markers.