Table 3.
List of RNA binding proteins associated with region 36 of the Lif 3′UTR
| Protein ID | Protein name | Gene name | 36 wt versus 36-No Significance | 36 wt versus 36-No Rel. levels | |
|---|---|---|---|---|---|
| Q13126 | S-methyl-5-thioadenosine phosphorylase | MTAP | 6.70E-06 | 2.11 | |
| Q9Y3U8 | 60S ribosomal protein L36 | RPL36 | 1.43E-05 | 2.05 | |
| P30040 | Endoplasmic reticulum resident protein 29 | ERP29 | 8.03E-05 | 1.91 | |
| P62942 | Peptidyl-prolyl cis-trans isomerase FKBP1A | FKBP1A | 0.0003 | 1.80 | |
| Q14019 | Coactosin-like protein | COTL1 | 0.0005 | 1.76 | |
| O75390 | Citrate synthase, mitochondrial | CS | 0.0012 | 1.68 | |
| P15121 | Aldose reductase | AKR1B1 | 0.0015 | 1.66 | |
| Q9Y281 | Cofilin-2 | CFL2 | 0.0019 | 1.64 | |
| Q02543 | ✩ | 60S ribosomal protein L18a | RPL18A | 0.0020 | 1.64 |
| P30041 | Peroxiredoxin-6 | PRDX6 | 0.0022 | 1.63 | |
| P42766 | ✩ | 60S ribosomal protein L35 | RPL35 | 0.0024 | 1.62 |
| Q96AG4 | Leucine-rich repeat-containing protein 59 | LRRC59 | 0.0041 | 1.57 | |
| Q01130 | ✩ | Serine/arginine-rich splicing factor 2 | SRSF2 | 0.0051 | 1.55 |
| P26447 | Protein S100-A4 | S100A4 | 0.0080 | 1.51 | |
| P60059 | Protein transport protein Sec61 subunit gamma | SEC61G | 0.0089 | 1.50 | |
| Q96AE4 | ✩ | Far upstream element-binding protein 1 | FUBP1 | 0.0090 | 1.50 |
| P09493 | Tropomyosin alpha-1 chain | TPM1 | 0.0099 | 1.49 | |
| P40616 | ADP-ribosylation factor-like protein 1 | ARL1 | 0.0104 | 1.48 | |
| Q99536 | Synaptic vesicle membrane protein VAT-1 homolog | VAT1 | 0.0115 | 1.47 | |
| P84098 | ✩ | 60S ribosomal protein L19 | RPL19 | 0.0120 | 1.47 |
| P61019 | Ras-related protein Rab-2A | RAB2A | 0.0127 | 1.47 | |
| Q9HAV7 | GrpE protein homolog 1, mitochondrial | GRPEL1 | 0.0127 | 1.47 | |
| O43396 | Thioredoxin-like protein 1 | TXNL1 | 0.0136 | 1.46 | |
| P26639 | Threonine--tRNA ligase, cytoplasmic | TARS | 0.0137 | 1.46 | |
| P09972 | Fructose-bisphosphate aldolase C | ALDOC | 0.0143 | 1.45 | |
| Q01581 | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | HMGCS1 | 0.0144 | 1.45 | |
| P63261 | Actin, cytoplasmic 2; Actin, cytoplasmic 2, N-terminally processed | ACTG1 | 0.0152 | 1.45 | |
| Q99497 | ✩ | Protein DJ-1 | PARK7 | 0.0180 | 1.43 |
| P16989 | ✩ | DNA-binding protein A | CSDA | 0.0192 | 1.42 |
| P06748 | ✩ | Nucleophosmin | NPM1 | 0.0212 | 1.41 |
| Q9BTT0 | Acidic leucine-rich nuclear phosphoprotein 32 family member E | ANP32E | 0.0221 | 1.41 | |
| P39023 | ✩ | 60S ribosomal protein L3 | RPL3 | 0.0227 | 1.41 |
| P13693 | Translationally-controlled tumor protein | TPT1 | 0.0267 | 1.39 | |
| P41567 | ✩ | Eukaryotic translation initiation factor 1 | EIF1 | 0.0270 | 1.39 |
| P49207 | ✩ | 60S ribosomal protein L34 | RPL34 | 0.0290 | 1.38 |
| Q9Y266 | Nuclear migration protein nudC | NUDC | 0.0305 | 1.38 | |
| Q15020 | ✩ | Squamous cell carcinoma antigen recognized by T-cells 3 | SART3 | 0.0331 | 1.37 |
| P09429 | High mobility group protein B1; Putative high mobility group protein B1-like 1 | HMGB1 | 0.0364 | 1.36 | |
| P40429 | 60S ribosomal protein L13a; Putative 60S ribosomal protein L13a-like | RPL13A | 0.0365 | 1.36 | |
| O43747 | AP-1 complex subunit gamma-1 | AP1G1 | 0.0400 | 1.35 | |
| Q00577 | Transcriptional activator protein Pur-alpha | PURA | 0.0410 | 1.35 | |
| P27635 | 60S ribosomal protein L10 | RPL10 | 0.0414 | 1.34 | |
| P00558 | Phosphoglycerate kinase 1 | PGK1 | 0.0462 | 1.33 | |
| P22314 | Ubiquitin-like modifier-activating enzyme 1 | UBA1 | 0.0473 | 1.33 | |
| Q9H0U4 | Ras-related protein Rab-1B | RAB1B | 0.0475 | 1.33 | |
| P61106 | ✩ | Ras-related protein Rab-14 | RAB14 | 0.0495 | 1.32 |
| P49588 | Alanine--tRNA ligase, cytoplasmic | AARS | 0.0503 | 1.32 | |
| O75915 | ✩ | PRA1 family protein 3 | ARL6IP5 | 0.0505 | 1.32 |
| P55795 | Heterogeneous nuclear ribonucleoprotein H2 | HNRNPH2 | 0.0523 | 1.32 | |
| P30086 | Phosphatidylethanolamine-binding protein 1; Hippocampal cholinergic neurostimulating peptide | PEBP1 | 0.0533 | 1.32 | |
| P68036 | Ubiquitin-conjugating enzyme E2 L3 | UBE2L3 | 0.0580 | 1.31 | |
| Q9UQE7 | Structural maintenance of chromosomes protein 3 | SMC3 | 0.0583 | 1.31 |
RNAs of region 36 (‘R36 wt’) and its counterpart ARE-null region 36 (‘R36-No’) were used for RNA binding assays. Bound proteins were identified by quantitative mass spectrometry analysis and relative ratios were determined using total sequence reads for region ‘R36 wt’ and region ‘R36-No’. RNA binding proteins (stars) are indicated as identified by GO pathway analysis (see Additional file 7: File S2). The significance is the significance A P-value as determined by the Perseus software, defining the likelihood of a protein being enriched compared to the background distribution.