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Table 1 Characterizing concepts for clusters identified through LASSO analysis.

From: Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease

Cluster

Subcluster

Characteristic

Biological Concepts (Up)

Biological Concepts (Down)

1

overall

Atrophy

-

Cyclins

1

1A

Atrophy – PABPN1 overexpression

Amino acyl tRNA synthetases, spermidine, polyamines, spermine, eukaryotic initiation factors

Platelet-derived growth factor, transforming growth factor-beta, insulin-like growth factor binding proteins

1

1B

EOM-specific

Adipocytes, acyl CoA dehydrogenase

Cyclins, keratin, cyclin-dependent kinases

2

overall

Dystrophy/myositis

Troponin, matrix metalloproteases

Mitogen activated protein kinases, insulin, ERK1 acitivity, phosphorylation

2

2A

Dystrophin defiency in EOM muscle

Troponin

-

2

2B

Myositis

Chemokine, chemokine receptor

-

2

2C

Regeneration

T-lymphocyte, phosphotransferases, phosphorylation, mitogen-activated protein kinases, integrins, cell cycle

Cullin proteins, mitogen-activated protein kinases, ligase

2

2D

Differentiation

Troponin, tropomyosin, nemaline myopathies, sarcomeres, myosin heavy chain, calsequestrin

Inhibitor of differentiation proteins, E2F transcription factors, proteoglycan, cell cycle proteins

2

2E

Ky-mutant/diverse

Leptin, desaturase, myosin heavy chains, neural cell adhesion molecules

Mitogen-activated protein kinases

3

overall

Ageing

Heterogeneous nuclear ribonucleoproteins, protein sumoylation, small nuclear ribonucleoprotein

-

  1. Concepts are shown separately for the down and up regulated gene lists. The column "Characteristic" gives a description of the studied phenomena in the cluster.