Table 3. Analysis of the high-ranking co-expression sets from Arabidopsis and rice using the Pfam-based predictor.
| Pfam ID | Predicted | Score (%) | Number of genes | Common protein name | Name used in working model | Related function | |
| Os | At | ||||||
| Golgi apparatus | |||||||
| PF03016 | GO | 100 | 4 | 6 | GT47 | GT47 | Glycosyltransferase |
| PF03360 | GO | 100 | 4 | 2 | GT43 | GT43 | Glycosyltransferase |
| PF01501 | GO | 80 | 3 | 4 | GT8, GAUT/GATL | IRX8; PARVUS | Glycosyltransferase |
| PF01501 | GO | 80 | 0 | 2 | GT8, PGSIP | PGSIP | Glycosyltransferase |
| PF01762 | GO | 67 | 3 | 1 | GT31 | GT31 | Glycosyltransferase |
| PF04577 | no data | 0 a) | 3 | 0 | GT61 | GT61 | Glycosyltransferase |
| PF03214 | GO | 100 | 2 | 0 | GT75 | RGP | UDP-arabinose mutase |
| PF03141 | GO | 92 | 2 | 1 | Putative methyltransferase | DUF248 | methylation |
| PF04669 | no data | 0 a) | 1 | 5 | DUF579 | DUF579 | unknown |
| PF03138 | GO | 55 | 2 | 2 | DUF246 | DUF246 | unknown |
| PF03005 | V/PL | 50/50 a) | 8 | 5 | DUF231 | DUF231 | acetylation |
| PF07779 | no data | 0 a) | 4 | 1 | O-acetyltransferase-related | Cas1P | acetylation |
| PF03151 | GO | 38 a) | 6 | 9 | Triose-phosphate transporter | TPT | NDP-sugar transport |
| PF01370 | GO | 13 a) | 4 | 5 | epimerase | UXS | epimerase |
| Plasma Membrane (extracellular) | |||||||
| PF00071 | PM | 78 | 5 | 7 | ROP, RAB GTPase | Rac | signaling/vesicle |
| PF00025 | PM | 57 | 2 | 1 | ADP-ribosylation GTPase | unknown/vesicle | |
| PF00612 | PM | 71 | 3 | 7 | IQ protein | IQ | signaling |
| PF00069 | PM | 70 | 11 | 10 | protein kinase | signaling | |
| PF00560, PF08263, PF00069 | PM | 80 | 3 | 5 | LRR family | LRR | signaling |
| PF00786 | PM | 100 | 1 | 2 | ROP interactive CRIB | RIC | signaling |
| PF02469 | PM | 82 | 9 | 4 | Fasciclin-like AGP | FAS | signaling |
| PF00182 | EX | 67 | 1 | 2 | GH19; chitinase-like | CTL | Glycosyl hydrolase |
| PF00295 | PM | 50 | 3 | 5 | GH28; Polygalacturonase | Glycosyl hydrolase | |
| PF07983 | PM | 100 | 2 | 3 | GH17; β-(1;3)-glucanase | Glycosyl hydrolase | |
| PF00759 | PM | 80 | 3 | 3 | GH9; cellulase | Glycosyl hydrolase | |
| PF07731, PF00394, PF07732 | PM | 57 | 4 | 6 | putative laccase | lignin formation | |
| PF03552 | PM | 60 | 8 | 3 | cellulose synthase | Glycosyltransferase | |
| PF04833 | PM | 100 | 2 | 1 | COBRA | GPI anchored | |
| PF02298 | PM | 78 | 6 | 4 | plastocyanin-like | GPI anchored | |
| PF00097 | PM | 51 | 12 | 8 | zinc finger | unknown | |
| PF06749 | PM | 100 | 2 | 2 | DUF1218 | unknown | |
| PF00190 | EX | 75 | 2 | 3 | Germin-like | unknown | |
| PF07058 | PM | 67 | 0 | 1 | Myosin HC-like | unknown | |
| PF00786, PF00620 | PM | 71 | 0 | 1 | RhoGAP | signaling | |
| PF07320 | PM | 78 | 10 | 0 | Hairpin-induced | unknown | |
| Nucleus | |||||||
| PF00249 | NC | 96 | 6 | 10 | MYB | MYB | Transcription |
| PF00010 | NC | 81 | 1 | 7 | bHLH (MYC) | MYC | Transcription |
| PF02365 | NC | 94 | 4 | 9 | NAC | NAC | Transcription |
| PF00642 | NC | 83 | 2 | 3 | dTIS | unknown | |
| PF04640 | no data | 0 | 1 | 0 | DUF597 | unknown | |
| PF00514 | NC | 54 | 3 | 1 | armadillo/beta-catenin repeat | unknown | |
| PF00719 | NC | 50 | 2 | 0 | PRLI-interacting factor | unknown | |
| PF04852 | NC | 100 | 0 | 4 | LSH | unknown | |
| Other components | |||||||
| PF00141 | V | 38 | 11 | 3 | peroxidase | lignin formation | |
| PF00026 | EX/PM | 33/33 | 1 | 1 | aspartyl protease | unknown | |
| PF01419 | NC/PL | 40/40 | 1 | 1 | jacalin lectin | unknown | |
| PF03999 | Cytoskeleton | 100 | 3 | 1 | MAP65-8 | unknown | |
| PF04784 | PL | 67 | 1 | 1 | DUF547 | unknown | |
| PF00240, PF02179 | - | 7 | 1 | Ubiquitin domain | unknown | ||
| PF00657 | V | 64 | 2 | 1 | Lipase, GDSL domain | lignin formation | |
| PF06814 | V | 50 | 3 | 1 | Transmembrane receptor | signaling | |
Groups of protein with the same Pfam domains were found in co-expression dataset. The table shows groups, where at least one gene exhibited an average MR of less than 70. The number of genes corresponding to each Pfam is from the entire co-expression set in Arabidopsis (Table S1) and rice (Table S3). The AGI and RAP codes are listed in Table S8. The predicted location and score are shown according to the Pfam-based predictor. Abbreviations for subcellular compartments are the same as in Table 2.
a)PF01370, PF03005, PF04669, PF03151, PF4577, and PF07779 proteins have been observed in Golgi apparatus (unpublished data) [82]. Based on the references they were categorized into Golgi apparatus, although they showed a low score by PFANTOM.