Table 1.

Genes commonly downregulated upon shRNA knockdown in MM cell lines

GeneGene nameCategoryJJN3U266KMS18
BIRC3 Baculoviral IAP repeat containing 3 NF-κB pathway, negative regulator + + + 
NFKBIA IκBα NF-κB pathway, negative regulator + + + 
TNFAIP3 TNFα-induced protein 3 NF-κB pathway, negative regulator + + + 
NFKBIE NF-κB inhibitor epsilon NF-κB pathway, negative regulator + + + 
RELA RELA subunit (target of shRNA) NF-κB pathway, subunit + + + 
RELB RELB subunit NF-κB pathway, subunit + + + 
IKBKE Inhibitor of NF-κB kinase subunit ε NF-κB pathway, negative regulator  + + 
NFKB2 NF-κB2, p100/p52 subunit NF-κB pathway, subunit  + + 
NFKB1 NF-κB1, p105/p50 subunit NF-κB pathway, subunit  + + 
IL27RA IL-27 receptor subunit α Cytokine/chemokine (receptor) + + + 
IL21R IL-21 receptor Cytokine/chemokine (receptor) +  + 
IL4R IL-4 receptor Cytokine/chemokine (receptor) +  + 
CD70 TNFSF7, ligand for CD27 Immune response/TNF receptor family member  + + 
CD83 CD83 molecule Immune response/antigen presentation + + + 
JAM2 Junctional adhesion molecule, CD322 Adhesion/migration + + + 
ICAM1 Intercellular adhesion molecule 1 Adhesion/migration  + + 
FAS CD95, Fas cell surface death receptor Apoptosis, pro +  + 
DOCK10 Dedicator of cytokinesis 10 Signaling + +  
PTGER4 Prostaglandin E receptor 4 Signaling +  + 
CAMK4 Calcium/calmodulin-dependent protein kinase IV Signaling/calcium +  + 
NFE2L3 Nuclear factor, erythroid 2-like 3 Cell cycle/proliferation (control) + + + 
GINS2 GINS complex subunit 2 Cell cycle/proliferation + +  
CDCA7 Cell division cycle-associated protein 7 Cell cycle/proliferation + +  
CDC25A Cell division cycle 25A Cell cycle/proliferation + +  
CCND1 Cyclin D1, BCL1, BCL-1 oncogene Cell cycle/proliferation (control) + +  
MIR30A microRNA 30A Posttranscriptional regulation/microRNA + + + 
MYB c-Myb, MYB proto-oncogene, transcription factor Transcriptional regulation/transcription factor + +  
SLC25A43 Solute carrier family 25 member 43 Metabolism +  + 
GALNT6 Polypeptide N-acetylgalactosaminyltransferase 6 Protein metabolism/glycosylation +  + 
BCAT1 Branched chain amino acid transaminase 1 Metabolism + +  
KHDRBS3 KH RNA binding domain cont., signal transduction associated 3 RNA metabolism + +  
APOBEC3B Apolipoprotein B messenger RNA editing enzyme catalytic subunit 3B RNA metabolism + +  
MSH2 MutS homolog 2, DNA mismatch repair protein Msh2 DNA repair + +  
AP3M2 Adapter-related protein complex 3 subunit μ 2 Intracellular trafficking/transport + +  
SCRN1 Secernin 1 Intracellular trafficking/transport + +  
RFTN1 Raftlin, lipid raft linker 1 Intracellular trafficking/transport +  + 
UNC13C Unc-13 homolog C Intracellular trafficking/transport  + + 
WWC3 WWC family member 3 Intracellular trafficking/transport  + + 
MTCL1 Microtubule crosslinking factor 1 Cytoskeleton + +  
NRM Nurim, nuclear envelope membrane protein Cytoskeleton/nuclear + +  
IGLL5 Immunoglobulin λ–like polypeptide 5 Immunoglobulin genes +  + 
GeneGene nameCategoryJJN3U266KMS18
BIRC3 Baculoviral IAP repeat containing 3 NF-κB pathway, negative regulator + + + 
NFKBIA IκBα NF-κB pathway, negative regulator + + + 
TNFAIP3 TNFα-induced protein 3 NF-κB pathway, negative regulator + + + 
NFKBIE NF-κB inhibitor epsilon NF-κB pathway, negative regulator + + + 
RELA RELA subunit (target of shRNA) NF-κB pathway, subunit + + + 
RELB RELB subunit NF-κB pathway, subunit + + + 
IKBKE Inhibitor of NF-κB kinase subunit ε NF-κB pathway, negative regulator  + + 
NFKB2 NF-κB2, p100/p52 subunit NF-κB pathway, subunit  + + 
NFKB1 NF-κB1, p105/p50 subunit NF-κB pathway, subunit  + + 
IL27RA IL-27 receptor subunit α Cytokine/chemokine (receptor) + + + 
IL21R IL-21 receptor Cytokine/chemokine (receptor) +  + 
IL4R IL-4 receptor Cytokine/chemokine (receptor) +  + 
CD70 TNFSF7, ligand for CD27 Immune response/TNF receptor family member  + + 
CD83 CD83 molecule Immune response/antigen presentation + + + 
JAM2 Junctional adhesion molecule, CD322 Adhesion/migration + + + 
ICAM1 Intercellular adhesion molecule 1 Adhesion/migration  + + 
FAS CD95, Fas cell surface death receptor Apoptosis, pro +  + 
DOCK10 Dedicator of cytokinesis 10 Signaling + +  
PTGER4 Prostaglandin E receptor 4 Signaling +  + 
CAMK4 Calcium/calmodulin-dependent protein kinase IV Signaling/calcium +  + 
NFE2L3 Nuclear factor, erythroid 2-like 3 Cell cycle/proliferation (control) + + + 
GINS2 GINS complex subunit 2 Cell cycle/proliferation + +  
CDCA7 Cell division cycle-associated protein 7 Cell cycle/proliferation + +  
CDC25A Cell division cycle 25A Cell cycle/proliferation + +  
CCND1 Cyclin D1, BCL1, BCL-1 oncogene Cell cycle/proliferation (control) + +  
MIR30A microRNA 30A Posttranscriptional regulation/microRNA + + + 
MYB c-Myb, MYB proto-oncogene, transcription factor Transcriptional regulation/transcription factor + +  
SLC25A43 Solute carrier family 25 member 43 Metabolism +  + 
GALNT6 Polypeptide N-acetylgalactosaminyltransferase 6 Protein metabolism/glycosylation +  + 
BCAT1 Branched chain amino acid transaminase 1 Metabolism + +  
KHDRBS3 KH RNA binding domain cont., signal transduction associated 3 RNA metabolism + +  
APOBEC3B Apolipoprotein B messenger RNA editing enzyme catalytic subunit 3B RNA metabolism + +  
MSH2 MutS homolog 2, DNA mismatch repair protein Msh2 DNA repair + +  
AP3M2 Adapter-related protein complex 3 subunit μ 2 Intracellular trafficking/transport + +  
SCRN1 Secernin 1 Intracellular trafficking/transport + +  
RFTN1 Raftlin, lipid raft linker 1 Intracellular trafficking/transport +  + 
UNC13C Unc-13 homolog C Intracellular trafficking/transport  + + 
WWC3 WWC family member 3 Intracellular trafficking/transport  + + 
MTCL1 Microtubule crosslinking factor 1 Cytoskeleton + +  
NRM Nurim, nuclear envelope membrane protein Cytoskeleton/nuclear + +  
IGLL5 Immunoglobulin λ–like polypeptide 5 Immunoglobulin genes +  + 
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