Table 2.

Clusters of up-regulated and down-regulated genes in the different silencing experiments

Downregulated in RB1-silenced cells	Upregulated in RB1-silenced cells	Downregulated in RB2/P130-silenced cells	Upregulated in RB2-silenced cells	Downregulated in P107-silenced cells	Upregulated in P107-silenced cells
Chromatin and DNA-related  Telomerase RNA component (TERC)a  Histone cluster 1, H2ak  Histone cluster 1, H2bl  Histone cluster 1, H2bn  Deoxythymidylate kinase (thymidylate kinase)	DNA repair  ATM interactor  Alphaa	Chromatin and DNA-related  Histone cluster 1, H1a deoxythymidylate kinase (thymidylate kinase)	Chromatin and DNA-related  MBD4a  Topoisomerase (DNA) II alpha	Chromatin and DNA-related  Laminin, beta 1	DNA repair  ATM interactor alphaa  Thalassemia/mental retardation syndrome  X-linked
RNA processing  Vault RNA 1–2  Small nucleolar RNA, H/ACA box 75 small nucleolar RNA, C/D box 116-22 RNA, U4 small nuclear 2 RNA, U5D small nuclear//RNA, U5D small nuclear RNA, U11 small nuclear small Cajal body-specific RNA 1 small Cajal body-specific RNA 23	RNA processing  Nucleolin  Nucleoporin	RNA processing  Vault RNA 1-2 small nucleolar RNA, H/ACA box 33 small nucleolar RNA, C/D box 52 small nucleolar RNA, C/D box 78 small nucleolar RNA, C/D box 113-4 small nucleolar RNA, C/D box 116-29 RNA, U5D small nuclear//RNA, U5D small nuclear small Cajal body-specific RNA 23	DNA repair  DNA cross-link repair 1a  Excision repair cross complementing  Rodent repair deficiency complementation group 5 ATM  interactora  ATRX  RAD50 homolog  X-ray repair complementing defective repair in Chin  Hamster cells 5 DNA-damage-inducible transcript 3  Apoptosis inhibitor 5  XIAP-associated 1 Fanconi anemia complementation group I	RNA processing  Vault RNA 1–2 small nucleolar RNA, H/ACA box 59 small nucleolar RNA, C/D box 59B small nucleolar RNA, H/ACA box 75 small nucleolar RNA, C/D box 78 small nucleolar RNA, C/D box 116-22	Cytoskeleton and matrix  Collagen, type XI, alpha 1 actin keratin 7 cadherin 13, H-cadherin (heart) ankyrin repeat domain 36B
Protein synthesis  Ribosomal protein L22-like 1  Ribosomal protein L29  Ribosomal protein S7  Eukaryotic translation initiation factor 4A2	Protein synthesis  Eukaryotic translation initiation factor 2C, 4  Eukaryotic translation initiation factor 4A3  Eukaryotic translation initiation factor 4B	Redox pathway  Glutathione S-transferase mu 1  Glutathione S-transferase mu 4  Glutathione S-transferase theta 2  Cytochrome c oxidase subunit VIIb	RNA processing Pol (RNA) II pol B  TAF2 RNA TATA box binding RRN3 RNA Polymerase I transcription factor  Homolog poly(A) pol alpha	Protein synthesis eukaryotic translation initiation factor 4A2  Valyl-tRNA synthetase	Growth factor paths Keratinocyte growth factor-like protein 1  Cytokine-like 1
Redox pathway  Glutathione S-transferase mu 5 thioredoxin  Cytochrome c oxidase subunit VIIb  NADH dehydrogenase, subunit 6 (complex I) dehydrogenase/reductase (SDR family) member 7B	Cytoskeleton  Collagen, type VI, alpha 3 collagen, type VIII, alpha 2 collagen, type X, alpha 1	Cytoskeleton and matrix  Integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)  Syndecan 4  Protocadherin 10 laminin, beta 1 tubulin, alpha 1c	Protein synthesis  eIF3E  eIF4B  eIF5B  eIF2, 2 beta  eF Tu GTP  Ribosomal S3A  Ribosomal L7  Ribosomal L14  Ribosomal RNA  Processing 7 A	Redox pathway  Glutathione S-transferase mu 1  Glutathione S-transferase mu
Cytoskeleton and matrix  Keratin-associated protein 1-3  Keratin-associated protein 4-7  Keratin-associated protein 4-12	Growth factor paths  PDGFCa Keratinocyte growth factor-like protein 1 interferon, alpha-inducible protein 6  Insulin-like growth factor 2  Insulin-like growth factor 2 receptora	Growth factor paths  Cellular retinoic acid binding protein 2 transforming growth factor, beta 2 fibroblast growth factor 5 tumor necrosis factor receptor superfamily, member	Redox pathway  Thioredoxin Red 1  Catalase SOD2 Mt glutathione peroxidase 8	Cytoskeleton and matrix  Fibronectin type III domain containing 4 proteoglycan 4
Growth factor paths  Fibroblast growth factor 5  Cellular retinoic acid binding protein 2	Miscellaneous  Neuroblastoma breakpoint family, member 10 neuroblastoma breakpoint family, member 9 neuroblastoma breakpoint family, member 1	Miscellaneous  Contactin-associated protein-like 3	Growth factor paths  Keratinocyte growth factor-like protein 1  Angiopoietin 1  FGF7  IGF2	Miscellaneous  Contactin-associated protein-like 3

The table shows some clusters of genes that may be related to some biological features of MSCs (self-renewal, senescence, apoptosis and DNA repair proficiency). ^aGenes that were selected for real-time RT-PCR validation of microarray analysis