- MAX dimerization proteins (MXD)
- Membrane-associated ring fingers (MARCH)
- Metalloprotein database The Scripps Research Institute
- Metallothioneins (MT)
- Mex-3 homologs (MEX3)
- Mitochondrial respiratory chain complex
- Mitochondrial ribosomal proteins (MRP)

- Mitogen-activated protein kinase cascade (MAP#K)
- MOB kinase activators (MOB)
- Mucins (MUC)

- Myocyte enhancer factors (MEF2)
- Myosins
- Myosin binding proteins (MYBP)
- Na+/K+ transporting ATPase interacting (NKAIN)
- N(alpha)-acetyltransferase subunits (NAA)
- N-terminal EF-hand calcium binding proteins (NECAB)
- ncRNAs (non-protein coding RNAs)

- NOL1/NOP2/Sun domain containing (NSUN)
- Nuclear factor of activated T-cells (NFAT)
- Nuclear receptors
- Nucleotide-binding domain and leucine rich repeat containing (NLR)
- Nudix motif-containing (NUDT)

- Olfactory receptors (OR)
- Opsins (OPN)
- ORAI calcium release-activated calcium modulators (ORAI)
- Oxysterol binding proteins (OSBP)
- Paraneoplastic Ma antigens (PNMA)
- Parkinson disease
- Patatin-like phospholipase domain containing (PNPLA)
- Paired boxes (PAX)
- Pellino homologs (PELI)
- Peptidyl arginine deiminases (PADI)
- Perilipins (PLIN)
- PHD-type zinc fingers (PHF)
- Phosphodiesterases (PDE)
- Plexins (PLXN)
- Poly (ADP-ribose) polymerases (PARP)
- Polycomb group ring fingers (PCGF)
- Potassium channels (KCN)

- POTE ankyrin domain containing (POTE)
- Prenyltransferase alpha subunit repeat containing (PTAR)
- Proline-rich transmembrane proteins (PRRT)
- Prostate and testis expressed (PATE)
- Proteasome (prosome, macropain) subunits (PSM)

- Protein arginine methyltransferases (PRMT)

- Protein disulfide isomerases (PDI)
- The Protein Kinase Resource
- Protein phosphatase 1, regulatory (inhibitor) subunits (PPP1R)

- Protein phosphatase catalytic subunits (PPP)
- Protein phosphatase, Mg2+/Mn2+ dependent (PPM)
- Protein tyrosine phosphatases (PTP)
, including dual specificity phosphatases
- Proteoglycans
- Protocadherins (PCDH)
- Pseudoautosomal regions
- Purinergic receptors (P2R)
