Table 5.

Proteins in U-2OS assigned to eleven subpatterns. For each protein, we calculated the distance from it to founders of subpatterns and classified it to the subpattern that has the shortest distance.

	Structure	Proteins classified with this approach	Previously classified
1	COPI	SMIM19, ERLIN1
2	COPII	ZNF155, SYK, PTPRZ1, ATP7A, CTSH, COL11A1, MMAA	ZNF155, SYK, PTPRZ1, ATP7A
3	Caveolae	VIM	IFI6, ACAA1, SERPINA4, ASB6
4	Coated pits		NAP1L5
5	Early Endosomes	RAB5C, NAP1L5	RAB5C, COL11A1, MMAA
6	Late Endosomes	KIAA0430, PANK2, MAP3K15, B4GALT1, OSBP2, SPARC, HAP1, OPTN, RPL23, DTX3L, CD300LG, NYAP1, ASB6	KIAA0430, PANK2, MAP3K15, B4GALT1, OSBP2, SPARC, HAP1, OPTN, RPL23, PHB, DIABLO, CASP8, 1_Mar, CTSH, FNDC9, SEC31A, GLUL, MRPL9, ARFGAP2, HSPA9, KDM5A, ALDH18A1, RALGAPA1, COMT, TAOK3, HJURP, TREM2, VIM, PSMB4, ERLIN1, TOMM70A
7	Lysosomes	PDZK1IP1, ACAA1, SERPINA4, ACADM, ALDH18A1, PSMB4	PDZK1IP1, ZBTB38, CACFD1, NYAP1
8	Peroxisomes
9	RNP bodies	PHB, DIABLO, HSPA9, COMT	FBXO15, PDE5A, CD300LG, ACADM, KLHDC8B, APOO, TOP1MT, SAMD9, IRF3
10	Recycling Endosomes	CASP8, 1_Mar, ZBTB38, FNDC9, IFI6, SEC31A, GLUL, MRPL9, FBXO15, ARFGAP2, PDE5A, KDM5A, KLHDC8B, APOO, TOP1MT, SAMD9, RALGAPA1, CACFD1, IRF3, TAOK3, HJURP, ARID4A, TREM2, TOMM70A	DTX3L, SMIM19
11	Retromer		1–9, ARID4A