The list of positive hits from the shRNA screen sorted by their known cellular functions
| Gene name . | Symbol . | Activities . | Processes involved, known . | Positive hits . | Confirmation . |
|---|---|---|---|---|---|
| Gene expression regulation | |||||
| Splicing factor proline/glutamine-rich | SFPQ | Associated with polypyrimidine tract-binding protein | Transcription and pre-mRNA processing | 1 | N/A |
| Chromodomain helicase DNA-binding protein 1 | CHD1 | Binds to DNA helicase | Chromatin assembly or disassembly, transcription | 1 | Confirmed |
| SPANX-b, c, and d | SPANX | Unknown | Regulates transcription and translation, spermatogenesis | 1 | N/A |
| Cellular repressor of adenovirus E1A protein-stimulated genes 1 | CREG1 | Antagonizes transcriptional activation of E1A protein | Transcriptional control of cell growth and differentiation | 1 | N/A |
| Metabolic regulation | |||||
| Asparagine-linked glycosylation 5 homolog | ALG5 | Dolichyl-phosphate beta-glucosyltransferase activity | N-glycan biosynthesis | 1 | N/A |
| 3-hydroxybutyrate dehydrogenase, type 2 | BDH2 | Dehydrogenase/reductase enzyme | Fatty acid beta-oxidation | 2 | Confirmed |
| Cathepsin K | CTSK | Cysteine proteinase | Proteolysis, tumor invasiveness, bone remodeling | 1 | Confirmed |
| Peroxiredoxin 3 | PRDX3 | Peroxidase activity, alkyl hydroperoxide reductase activity | Activation of NF-kappaB transcription factor, antioxidant | 1 | Confirmed |
| Protein kinases | |||||
| Serine threonine kinase 39 | STK39 | Protein serine/threonine kinase activity | Mediates stress-activated signals | 1 | N/A |
| Protein kinase C, nu | PRKCN | Protein serine/threonine kinase activity | Intracellular signaling cascade | 1 | N/A |
| Serine/threonine protein kinase MST4 | MASK | Protein serine/threonine kinase activity | Regulation of apoptosis, can be cleaved by caspase-3 | 1 | N/A |
| Cell signaling related | |||||
| NCK adaptor protein 1 | NCK1 | Contains SH2 and SH3 domains, cytoskeletal adaptor | Intracellular signaling cascade, positive regulation of actin filament polymerization | 1 | Confirmed |
| NCK-associated protein 1 | NCKAP1 | Interacts with Nck | Lamellipodium biogenesis, apoptosis | 1 | Confirmed |
| Transient receptor potential cation channel, subfamily C, member 6 | TRPC6 | Calcium channel activity | Calcium ion transport, calcium signaling | 1 | Confirmed |
| Interleukin 1 receptor antagonist | IL1RN | Inhibits the activities of interleukin 1 | Regulates immune and inflammatory responses | 1 | N/A |
| Cell death/stress related | |||||
| Hypoxia-inducible factor 1, alpha subunit | HIF1A | Transcription factor | Cellular and systemic homeostatic responses to hypoxia | 1 | Confirmed |
| DED containing | DEDD | Contains DED, regulation of apoptosis | Cell death | 1 | N/A |
| Transmembrane BAX inhibitor motif containing 1 | TMBIM1 | Contains BAX inhibitor motif | Cell death | 1 | N/A |
| Others | |||||
| Ubiquitin-conjugated enzyme, UBE2D3 | UBE2D3 | Ubiquitin-protein ligase activity | Ubiquitin-mediated proteolysis | 3 | Confirmed |
| Nidogen 2/osteonidogen | NID2 | A basement membrane protein | Adhesion, migration, differentiation, gene expression, and apoptosis | 1 | N/A |
| Mutated in colorectal cancers | MCC | Interacts with NFKBIB | Putative colorectal tumor suppressor gene | 1 | Confirmed |
| Complement component 1, q subcomponent-binding protein | C1QBP | Inhibit C1 activation | Play a role in serum complement system | N/A | |
| Ancient ubiquitous protein 1 | AUP1 | Unknown | Play a crucial role in the integrin alpha(IIb)beta(3) inside-out signaling | 1 | N/A |
| Stromal interaction molecule 1 | STIM1 | Unknown | Located in an important tumor-suppressor gene region, calcium signaling | 1 | N/A |
| Spastic ataxia of Charlevoix-Saguenay, sacsin | SACS | Unknown | Mutated in ARSACS | 1 | N/A |
| Similar to interferon-induced transmembrane protein 3, LOC144383 | N/A | Unknown | Unknown | 1 | N/A |
| Gene name . | Symbol . | Activities . | Processes involved, known . | Positive hits . | Confirmation . |
|---|---|---|---|---|---|
| Gene expression regulation | |||||
| Splicing factor proline/glutamine-rich | SFPQ | Associated with polypyrimidine tract-binding protein | Transcription and pre-mRNA processing | 1 | N/A |
| Chromodomain helicase DNA-binding protein 1 | CHD1 | Binds to DNA helicase | Chromatin assembly or disassembly, transcription | 1 | Confirmed |
| SPANX-b, c, and d | SPANX | Unknown | Regulates transcription and translation, spermatogenesis | 1 | N/A |
| Cellular repressor of adenovirus E1A protein-stimulated genes 1 | CREG1 | Antagonizes transcriptional activation of E1A protein | Transcriptional control of cell growth and differentiation | 1 | N/A |
| Metabolic regulation | |||||
| Asparagine-linked glycosylation 5 homolog | ALG5 | Dolichyl-phosphate beta-glucosyltransferase activity | N-glycan biosynthesis | 1 | N/A |
| 3-hydroxybutyrate dehydrogenase, type 2 | BDH2 | Dehydrogenase/reductase enzyme | Fatty acid beta-oxidation | 2 | Confirmed |
| Cathepsin K | CTSK | Cysteine proteinase | Proteolysis, tumor invasiveness, bone remodeling | 1 | Confirmed |
| Peroxiredoxin 3 | PRDX3 | Peroxidase activity, alkyl hydroperoxide reductase activity | Activation of NF-kappaB transcription factor, antioxidant | 1 | Confirmed |
| Protein kinases | |||||
| Serine threonine kinase 39 | STK39 | Protein serine/threonine kinase activity | Mediates stress-activated signals | 1 | N/A |
| Protein kinase C, nu | PRKCN | Protein serine/threonine kinase activity | Intracellular signaling cascade | 1 | N/A |
| Serine/threonine protein kinase MST4 | MASK | Protein serine/threonine kinase activity | Regulation of apoptosis, can be cleaved by caspase-3 | 1 | N/A |
| Cell signaling related | |||||
| NCK adaptor protein 1 | NCK1 | Contains SH2 and SH3 domains, cytoskeletal adaptor | Intracellular signaling cascade, positive regulation of actin filament polymerization | 1 | Confirmed |
| NCK-associated protein 1 | NCKAP1 | Interacts with Nck | Lamellipodium biogenesis, apoptosis | 1 | Confirmed |
| Transient receptor potential cation channel, subfamily C, member 6 | TRPC6 | Calcium channel activity | Calcium ion transport, calcium signaling | 1 | Confirmed |
| Interleukin 1 receptor antagonist | IL1RN | Inhibits the activities of interleukin 1 | Regulates immune and inflammatory responses | 1 | N/A |
| Cell death/stress related | |||||
| Hypoxia-inducible factor 1, alpha subunit | HIF1A | Transcription factor | Cellular and systemic homeostatic responses to hypoxia | 1 | Confirmed |
| DED containing | DEDD | Contains DED, regulation of apoptosis | Cell death | 1 | N/A |
| Transmembrane BAX inhibitor motif containing 1 | TMBIM1 | Contains BAX inhibitor motif | Cell death | 1 | N/A |
| Others | |||||
| Ubiquitin-conjugated enzyme, UBE2D3 | UBE2D3 | Ubiquitin-protein ligase activity | Ubiquitin-mediated proteolysis | 3 | Confirmed |
| Nidogen 2/osteonidogen | NID2 | A basement membrane protein | Adhesion, migration, differentiation, gene expression, and apoptosis | 1 | N/A |
| Mutated in colorectal cancers | MCC | Interacts with NFKBIB | Putative colorectal tumor suppressor gene | 1 | Confirmed |
| Complement component 1, q subcomponent-binding protein | C1QBP | Inhibit C1 activation | Play a role in serum complement system | N/A | |
| Ancient ubiquitous protein 1 | AUP1 | Unknown | Play a crucial role in the integrin alpha(IIb)beta(3) inside-out signaling | 1 | N/A |
| Stromal interaction molecule 1 | STIM1 | Unknown | Located in an important tumor-suppressor gene region, calcium signaling | 1 | N/A |
| Spastic ataxia of Charlevoix-Saguenay, sacsin | SACS | Unknown | Mutated in ARSACS | 1 | N/A |
| Similar to interferon-induced transmembrane protein 3, LOC144383 | N/A | Unknown | Unknown | 1 | N/A |
The positive colonies that have been confirmed by the “liquid culturing assay” (details in “Materials and methods” and Table S2) are indicated.
Positive hits indicates the number of positive colonies matching the same gene; N/A, not available (has not been tested); DED, death effector domain; and ARSACS, autosomal recessive spastic ataxia of Charlevoix-Saguenay.