Supplementary material for
Spectral Analyses of Protein-Protein Interactions in Drosophila melanogaster
by Christel Kamp and Kim Christensen

Subgraphs of nodes that form orbits of size 2 and that have degree >= 2 (black), orbits of size 2 of nodes with degree 2 have been omitted. The white nodes are the neighbors of duplicate nodes that may have more neighbors than shown. The nodes' labels are their identifiers from the Database of Interacting Proteins.
The following tables contain the information on the proteins shown in the figure extracted from the Database of Interacting Proteins and FlyBase.

Table 1: Proteins found in the 2-orbit with nodes of degree 10, both duplicates (bold) are male specific RNA (with corresponding polypeptides).

DIP ID	Protein name/description
DIP:17489N	CG11719-PA open reading frame, Mst98Ca,
	(Male-specific RNA 98Ca)
DIP:17490N	CG18396-PA open reading frame, Mst98Cb,
	(Male-specific RNA 98Cb)
DIP:17144N	CG4015-PA open reading frame, Fcp3C,
	(Follicle cell protein 3C)
DIP:18312N	CG17777-PA open reading frame
DIP:17051N	CG17666-PA open reading frame
DIP:17123N	CG15781-PA open reading frame
DIP:17121N	CG15032-PA open reading frame
DIP:17122N	CG15489-PA open reading frame
DIP:20125N	CG1981-PA open reading frame, Thd1,
	G/T-mismatch-specific-thymine-DNA-
	glycosylase, double-stranded DNA-binding,
	mismatch repair
DIP:20084N	CG13363-PA open reading frame
DIP:19658N	CG12212-PA open reading frame, peb,
	(pebbled),
	transcription factor activity
DIP:17485N	CG10154-PA open reading frame,
	structural constituent of peritrophic
	membrane, (sensu Insecta)

Table 3: Proteins found in a 3-orbit with nodes of degree 2, lines separate different orbits, bold proteins are duplicates. Note, that Mst98Ca and Mst98Cb form a 2-orbit of degree 10, too (cf. Tab. 1).

DIP ID	Protein name/description
DIP:20847N	CG8284-PA open reading frame, UbcD4,
	(Ubiquitin conjugating enzyme 4),
	ubiquitin conjugating enzyme activity,
	ligase activity,
	protein metabolism, ubiquitin cycle
DIP:23198N	CG30344-PA open reading frame
DIP:18933N	CG10862-PA open reading frame,
	ubiquitin conjugating enzyme activity,
	ligase activity,
	protein metabolism
DIP:18935N	CG8974-PA open reading frame,
	transcription regulatory activity,
	``nucleo-metabolism'', transcription,
DIP:18934N	CG32581-PA open reading frame,
	transcription regulatory activity,
	``nucleo-metabolism'', transcription
DIP:20125N	CG1981-PA open reading frame, Thd1,
	G/T-mismatch-specific-thymine-DNA-
	glycosylase, double-stranded DNA-binding,
	mismatch repair
DIP:19658N	CG12212-PA open reading frame, peb,
	(pebbled),
	transcription factor activity
DIP:20084N	CG13363-PA open reading frame
DIP:17489N	CG11719-PA open reading frame, Mst98Ca,
	(Male-specific RNA 98Ca)
DIP:17490N	CG18396-PA open reading frame, Mst98Cb,
	(Male-specific RNA 98Cb)

Table 5: Proteins found in the 2-orbit with nodes of degree 7, duplicates (bold) are constituents of the larval cuticle. Note, that peb, Thd1, and CG13363-PA also form a 3-orbit with respect to Mst98Ca and Mst98Cb (cf. Tab. 3)

DIP ID	Protein name/description
DIP:19748N	CG1252-PA open reading frame, Ccp84Ab,
	(cuticle cluster 7),
	structural constituent of larval cuticle,
	(sensu Insecta)
DIP:19749N	CG2360-PA open reading frame, Ccp84Aa,
	(cuticle cluster 8),
	structural constituent of larval cuticle,
	(sensu Insecta)
DIP:17392N	CG9949-PA open reading frame, sina,
	(seven in absentia),
	sensory organ development
DIP:18536N	CG6615-PA open reading frame, scaf6,
	RNA binding, nuclear mRNA splicing
	via spliceosome, spliceosome complex
DIP:20225N	CG2341-PA open reading frame, Ccp84Ad,
	(cuticle cluster 5),
	structural constituent of larval cuticle,
	(sensu Insecta)
DIP:17713N	CG15422-PA open reading frame
DIP:17492N	CG12723-PA open reading frame
DIP:17076N	CG6945-PA open reading frame
DIP:17488N	CG11505-PB open reading frame

Table 2: Proteins found in a 2-orbit with nodes of degree 3, lines separate different orbits, bold proteins are duplicates.

DIP ID	Protein name/description
DIP:18704N	CG2789-PA open reading frame,
	bonzodiazepine receptor activity,
	transporter activity,
	metabolism and transport
DIP:18703N	CG1341-PA open reading frame, Rpt1,
	endopeptidase activity, ATPase activity,
	proteolysis and peptidolysis
DIP:21261N	CG3173-PA open reading frame
DIP:20398N	CG12096-PA open reading frame
DIP:17864N	CG10694-PA open reading frame
	damaged DNA-binding, base excision repair
DIP:20457N	CG12405-PA open reading frame, Prx2540-1,
	(Peroxiredoxin 2540),
	peroxidase, antioxidant activity,
	defense response, oxygen species metabolism
DIP:20458N	CG12896-PA open reading frame,
	peroxidase activity
	defense response, oxygen species metabolism
DIP:20623N	CG9624-PA open reading frame
DIP:17811N	CG5576-PA open reading frame, imd,
	(immune deficiency),
	antimicrobial humoral response,
	(sensu Invertebrata)
DIP:17346N	CG12470-PA open reading frame
DIP:18389N	CG18779-PA open reading frame
DIP:18387N	open reading frame CG-10530/4-PA,
	Lcp65Ag1/Lcp65Ag2 protein,
	(larval cuticle protein),
	structural constituent of larval cuticle,
	(sensu Insecta),
	larval cuticle biosynthesis,
	(sensu Insecta)
DIP:18392N	CG2082-PA open reading frame,
	signal transduction
DIP:18391N	CG16978-PA open reading frame
DIP:18390N	CG12907-PA open reading frame

Table 4: Proteins found in the 4-orbit with nodes of degree 4, all duplicates (bold) are heat shock proteins (Hsp), released after heat shock or other stress.

DIP ID	Protein name/description
DIP:19548N	CG31366/18743-PA open reading frame,
	Hsp70A, (Heat shock protein 70A),
	heat, defense response,
	protein complex assembly and folding
DIP:19549N	CG31449/31359/6489-PA open reading frame,
	Hsp70B, (heat shock protein 70B),
	heat, defense response,
	protein complex assembly and folding
DIP:19551N	open reading frame CG31449-PA, Hsp70Ba,
	(heat shock protein 70Ba),
	heat, defense response,
	protein complex assembly and folding
DIP:19552N	CG5834-PA open reading frame, Hsp70Bbb,
	(heat shock protein 70Bbb)
DIP:18493N	CG7945-PA open reading frame,
	chaperone activity
DIP:20272N	CG5203-PA open reading frame, CHIP,
	chaperone activity, protein folding
	and metabolism
DIP:20308N	CG32130-PA open reading frame
DIP:18578N	CG13165-PA open reading frame