MuscleDBs

Introduction

Skeletal muscles have indispensable functions in human body and also possess prominent regenerative ability. The rapid emergence of Next Generation Sequencing (NGS) data in recent years offers us an unprecedented perspective to understand gene regulatory networks governing skeletal muscle development and regeneration. However, the data from public NGS database are often in raw data format or processed with different procedures, causing obstacles to make full use of them (Yuan et al., 2019) [1]. Herein, we have integrated all information about current databases developed to represent disparate and heterogeneous omics data (with a focus on transcriptomics data) generated for skeletal muscle in different species.

Databases

MuscleDB

Analysis of the model suggested that metabolic activation and recruitment of muscle fibers are closely related, but the degree of metabolic activation inferred from metabolite changes may differ from that of the fiber recruitment. Simulations with a mechanistic, mathematical model demonstrated that the activation as measured by metabolic response in single fibers is distinct from fiber recruitment that is characterized by the number (or mass) of each fiber type involved during a specific exercise. The results from this study underline the need for critical experiments that measure fiber recruitment and metabolism in order to simulate and quantify the contributions of type I and II fibers to the regulation of energy metabolism. Such experimental techniques could be used in combination with the computational model to investigate the relationships between the extents of metabolic activation, number of fibers recruited, and muscle groups engaged at different intensity exercise.

Summarized table of the databases

Database	Short description	Data type	Functionality	Statistics	Current status	Reference
BIOMD0000000248	Lai2007_O2_Transport_Metabolism.	The mathematical model simulates oxygen transport and metabolism in skeletal muscle in response to a step change from a warm-up steady state to a higher work rate corresponding to exercise at different levels of intensity: moderate (M), heavy (H) and very heavy (VH).	Lai et al., 2007 [2]	Relevant	Relevant	Relevant

Table1. Summarized table of the databases with transcriptomics data generated for skeletal muscle in different species.

References

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