Table 1.
Prioritization of candidate genes. Genes carrying SNPs with GERP score above 6 located in regulatory regions or having a predicted moderate or high impact on protein function
| Gene symbol | Gene name | Gene biotype | Regulatory SNP | Moderate or high impact SNPs | FOB QTL | IMPC2 | Gene ontology3 | Mammalian phenotype4 | Human disease5 | Expression6 | High number of SNPs7 | Validated by MGI8 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 4930441H08Rik | RIKEN cDNA 4930441H08 gene | lncRNA gene | L:1 PFR, F:0 | - | ✓ | |||||||
| 4930595O18Rik | RIKEN cDNA 4930595O18 gene | lncRNA gene | L:1 PFR, F:0 | - | ||||||||
| Aff3 | AF4/FMR2 family, member 3 | protein coding gene | - | L:1, F:0 | ✓ | |||||||
| Angpt1 | angiopoietin 1 | protein coding gene | L:1 TFBS, F:0 | - | ✓ | |||||||
| Atpsckmt | ATP synthase C subunit lysine N-methyltransferase | protein coding gene | L:0, F:1 TFBS | - | ||||||||
| Cpped1 | calcineurin-like phosphoesterase domain containing 1 | protein coding gene | L:1 PFR, F:0 | - | ||||||||
| Erc2 | ELKS/RAB6-interacting/CAST family member 2 | protein coding gene | L:0, F:1 E | - | ||||||||
| Gfra1 | glial cell line derived neurotrophic factor family receptor alpha 1 | protein coding gene | L:1 E, F:0 | - | ✓ | ✓ | ||||||
| Gm17131 | predicted gene 17,131 | pseudogene | L:0, F:1 PFR and CTCFBS | - | ||||||||
| Gm36633 | predicted gene, 36,633 | lncRNA gene | L:1 PFR, F:0 | - | ✓ | |||||||
| Fam237b | family with sequence similarity 237, member B | protein coding gene | - | L:1, F:0 | ✓ | |||||||
| Mast4 | microtubule associated serine/threonine kinase family member 4 | protein coding gene | L:1 PFR, F:1 PFR | - | ✓ | |||||||
| Or56b2j | olfactory receptor family 56 subfamily B member 2 J | polymorphic pseudogene | - | L:0, F:1 | ✓ | |||||||
| Pced1a | PC-esterase domain containing 1 A | protein coding gene | - | L:0, F:1 | ✓ | ✓ | ||||||
| Prr5l | proline rich 5 like | protein coding gene | L:1 PFR and OCR, F:0 | - | ✓ | ✓ | ||||||
| Serpine2 | serine (or cysteine) peptidase inhibitor, clade E, member 2 | protein coding gene | L:1 P, F:0 | - | ✓ | ✓ | ||||||
| Tecrl | trans-2,3-enoyl-CoA reductase-like | protein coding gene | - | L:0, F:1 | ✓ | ✓ | ||||||
| Tmem132d | transmembrane protein 132D | protein coding gene | L:0, F:1 PFR and CTCFBS | - | ✓ | |||||||
| Trim24 | tripartite motif-containing 24 | protein coding gene | - | L:1, F:0 | ✓ | |||||||
| Zfp536 | zinc finger protein 536 | protein coding gene | L:1 PFR, F:0 | - | ✓ | ✓ |
1 - E: enhancer, CTCFBS: CTCF binding site, P: promoter, PFR: promoter flanking region, TFBS: transcription factor binding site
2 - search term: abnormal adipose tissue amount
3 - search keywords: adipo, cholesterol, digestion, eating, energy, fat, feeding, glucose, glycogen, insulin, lean, leptin, lipid, lipoprotein, obese, olfactory, phagy, smell, storage, taste, thermogenesis
4 - search keywords: adipose, cholesterol, digestion, eating, energy, fat, fatigue, feeding, glucose, glycogen, insulin, lean, leptin, lipid, lipoprotein, obese, olfactory, phagy, smell, storage, taste, thermogenesis
5 - search keywords: cardio, diabetes, dystrophy, eating, feeding, glycemia, glycogen, heart, hypertension, insulin, lean, leptin, lipidemia, lipodystrophy, liver, muscular, obesity, olfactory, osteoarthritis, phagy, smell, taste, thermogenesis
6 - Differential gene expression (Microarray or RNA-seq)
7 - Supplementary Table S3
8 - SNP is present in Fat line and obese mouse NZO/HlLtJ or present in the Lean line and obesity resistant A/J mouse line