The autophagy interaction network of the aging model Podospora anserina

BMC Bioinformatics

Table 2 The ten most important proteins of the predicted PPI network

Module no.	Protein	Alias (no.	Ranks	Total	Effects in
(color code)	identifier	of interactions)	degree /	rank	knockout
			between.		yeast strains
3 (turquois)	Pa_3_5250	PaATG8 (22)	1 / 1	2	ne, aa, dv
2 (green)	Pa_5_5550	PaATG9 (13)	2 / 4	6	ne, aa, dv
1 (red)	Pa_4_9630	PaTOR (11)	4 / 2	6	TOR1: ne; TOR2: e
2 (green)	Pa_1_20610	PaATG3 (13)	3 / 6	9	ne, aa, dv
6 (ocher)	Pa_3_7690	PaYPT1 (9)	9 / 3	12	e
2 (green)	Pa_1_14210	PaATG11 (9)	8 / 8	16	ne, ma
3 (turquois)	Pa_4_7460	PaATG12 (10)	5 / 12	17	ne, aa, dv
6 (ocher)	Pa_5_4470	PaTRS130 (10)	6 / 13	19	e
2 (green)	Pa_5_5670	PaSEC24 (7)	16 / 9	25	e
2 (green)	Pa_7_10890	PaATG1 (6)	22 / 5	27	ne, aa, dv

The first column gives the module and its color according to Fig. 3. The column “Ranks” gives the ranks based on the degree and the betweenness. We summed up both values to a total rank and sort the table in descending order. The last column gives the most important effects on the yeast strain where the corresponding homologous gene had been knocked out [7]. Abbreviations: ne=non-essential, aa=autophagy absent, dv=decreased viability, e=essential, ma=mitophagy absent. For PaTOR, two homologs exist, TOR1 and TOR2. The protein identifiers were adopted from the P. anserina genome database [10]

ISSN: 1471-2105