Table 2. Molecular function of proteins associated with Htt-polyQ aggregates as identified by TAPI (N = 91) in Rattus norvegicus.

Functional Category	% of total	Gene/Protein Name
Protein Quality Control/ Chaperone	26%	ADRM1, CLTC, DDI2, DNAJA2, DNAJA4, DNAJB1, DNAJC7, HSP90AA1, HSPA8, LAP3, PPIA, PSMB2, PSMC1, PSMC2, PSMC3, RAD23B, SGTA, SQSTM1, SUMO2, UBQLN2, UBQLN4, UBXN7, USP7, VPS35
RNA/DNA binding*	37%	AARS2, AKAP81, ARL6IP4, ATP5A1, ATRX, DDX5, DYNC1H1, EIF4G1, EIF4G2, FASN, FUS, GIGYF2, HNRNPA3, HNRNPF, HNRNPH2, HNRNPM, HNRNPU, HSP90AA1, MATR3, NONO, NR3C1, PCBP1, PPIA, PRPF40A, PRRC2B, RBMS1, SF1, TDP-43, TCERG1, TCF20, TNRC6B, TUFM, XRN2, YTHDF1
Mitochondrial	18%	AARS2, ACAD9, ACSF2, ATP5A1, CLTC, ETFB, GLS, HADHA, IDH2, NDUFS7, OGDH, PCK2, PDHB, SUCLG2, TUFM
Endocytosis, Vessicle & Cytoskeletal Transport	14%	AAK1, ARL6IP4, ASAP1, CLINT1, CLTC, CNN2, DYNC1H1, MYO1D, NSFL1C, RAB10, SCYL2, TFG, VPS35
Other	15%	EP300, GNAO1, KPRP, LDHA, MAGED1, MLF2, PHGDH, PLEKHB2, PPP2R1A, SIK3, SFN, TGM3, THY1, YWHAB

Molecular function assignments were determined by gene ontology, RGD, and NCBI.

* RNA-binding was assigned in some cases on empirical data [99], thus classification does not necessarily imply primary function. Proteins in bold represent those that were placed in multiple categories, thus totals can exceed 100%. Rat ribosomal proteins Rpl6 and Rpl13a were excluded.