Data exported from Scaffold to Excel for further analysis

The resultant estimates of protein levels in each sample were then exported to Microsoft Excel (Microsoft Corp.). Following the removal of the trial injection data, paired two tail t-tests were carried out on the plus arsenite and minus arsenite samples separately. There were 316 protein clusters, of which 95 had no values recorded with the minus arsenite samples and 4 that had no values recorded in the plus arsenite samples. In order to get a general feel for the data, a liberal significance cut off point of p=0.1 was selected without a multiple testing correction. As some proteins were present at higher levels in the IgG samples, these were removed from further consideration. In addition to this, all proteins that were present in every UNR sample but absent in every IgG sample were considered, even if they were not considered significant by t-test (protein name shaded yellow). The proteins/protein clusters considered significant, by the parameters laid out above, from the HeLa minus arsenite samples are presented in Table 4.2B by p-value. The top 10 putative UNR interacting proteins are tabulated by t-test p-value with the total ion current values for each replicate (Table 4.2A). Likewise, the top ten putative UNR interacting proteins from the HeLa plus arsenite samples are presented in Table 4.2C and all putative interactors, by the criteria outlined above, are presented in Table 4.2D.

Table 4.2A: Top ten hits HeLa minus arsenite, by t-test p-value

Protein HeLa1 HeLa2 HeLa3 HeLa4 HeLa5 HeLa6 p-value

SSBP4 0 0 0 685800 555720 676130 0.0043 UNRIP 0 0 0 2243600 1895500 1477100 0.0137 HUWE1 0 0 0 386300 265730 425550 0.0175 NARR 0 0 0 1972000 1237800 1377100 0.0210 RPL23A 0 0 0 118830 67403 86181 0.0263 HSPD1 0 0 130270 40965 34231 150430 0.0352 LDB1 0 0 0 442690 308230 214140 0.0400 UNR 0 0 0 3420100 1988100 1163000 0.0799 RPS5 155490 45419 0 273250 228700 56890 0.0822 SQSTM1 0 38981 0 181450 443410 160790 0.0858

N.B. IgG samples shaded lilac, repeat 1-3 running left to right (HeLa1-HeLa3). The corresponding UNR samples are shaded green and also run left to right (HeLa4-HeLa6). The t-test p-values are for a two tailed paired t-test without multiple testing correction. Yellow shading denotes proteins that were recorded in UNR samples only. The full names for each protein can be found in Table 4.2B.

Table 4.2B: Putative UNR-interacting proteins from unstressed HeLa cells, by t-test p- value

Protein p-value

Cluster of U3KPY3_HUMAN Single-stranded DNA-binding protein 4 (Fragment)

GN=SSBP4 0.0043

Cluster of STRAP_HUMAN Serine-threonine kinase receptor-associated protein

GN=STRAP 0.0137

Cluster of HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 GN=HUWE1 0.0175 NARR_HUMAN Ras-related protein RAB34, isoform NARR GN=RAB34 0.0210 Cluster of K7EJV9_HUMAN 60S ribosomal protein L23a (Fragment) GN=RPL23A 0.0263 CH60_HUMAN 60 kDa heat shock protein, mitochondrial GN=HSPD1 0.0352 Cluster of LDB1_HUMAN Isoform 2 of LIM domain-binding protein 1 GN=LDB1 0.0400 Cluster of CSDE1_HUMAN Isoform 4 of Cold shock domain-containing protein

E1 GN=CSDE1 0.0799

M0R0F0_HUMAN 40S ribosomal protein S5 (Fragment) GN=RPS5 0.0822

Cluster of SQSTM_HUMAN Sequestosome-1 GN=SQSTM1 0.0858

LMO4_HUMAN LIM domain transcription factor LMO4 GN=LMO4 0.0872

Cluster of TFG_HUMAN Protein TFG GN=TFG 0.1878

Cluster of MYCB2_HUMAN E3 ubiquitin-protein ligase MYCBP2 GN=MYCBP2 0.2842 N.B. The t-test p-values are for a two tailed paired t-test without multiple testing correction. Yellow shading denotes proteins that were recorded in UNR samples only.

Table 4.2C: Top ten hits HeLa plus arsenite, by t-test p-value

HeLa7 HeLa8 HeLa9 HeLa10 HeLa11 HeLa12 p-value

DYNC1H1 0 0 2597900 778280 905160 3459800 0.0019 RPS2 121020 249370 111950 536230 704780 599190 0.0021 SSBP4 0 0 0 558350 425290 503750 0.0060 RPS3A 0 0 0 131180 172260 146250 0.0063 RPS4X 491630 569950 478130 1157600 1081000 1124200 0.0064 PRKDC 0 685150 6091400 797870 1753200 7197100 0.0094 HUWE1 0 0 0 667350 555970 458200 0.0114 LDB1 0 0 0 311660 268440 206310 0.0133 RPL28 0 0 175820 105510 160420 314300 0.0137 FAU 24481 23947 0 113530 101430 116240 0.0145

N.B. IgG samples shaded lilac, repeat 1-3 running left to right (HeLa7-HeLa9). The corresponding UNR samples are shaded green and also run left to right (HeLa10-HeLa12). The t-test p-values are for a two tailed paired t-test without multiple testing correction. Yellow shading denotes proteins that were recorded in UNR samples only. The full names for each protein can be found in Table 4.2D.

Table 4.2D: Putative UNR-interacting proteins from arsenite stressed HeLa cells, by t-test p- value

Protein p-value

Cluster of DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 GN=DYNC1H1 0.0019 Cluster of RS2_HUMAN 40S ribosomal protein S2 GN=RPS2 0.0021 Cluster of U3KPY3_HUMAN Single-stranded DNA-binding protein 4 (Fragment)

GN=SSBP4 0.0060

D6RG13_HUMAN 40S ribosomal protein S3a (Fragment) GN=RPS3A 0.0063 Cluster of RS4X_HUMAN 40S ribosomal protein S4, X isoform GN=RPS4X 0.0064 PRKDC_HUMAN DNA-dependent protein kinase catalytic subunit GN=PRKDC 0.0094 Cluster of HUWE1_HUMAN E3 ubiquitin-protein ligase HUWE1 GN=HUWE1 0.0114 Cluster of LDB1_HUMAN Isoform 2 of LIM domain-binding protein 1 GN=LDB1 0.0133 Cluster of H0YKD8_HUMAN 60S ribosomal protein L28 GN=RPL28 0.0137

RS30_HUMAN 40S ribosomal protein S30 GN=FAU 0.0145

A9Z1X7_HUMAN Serine/arginine repetitive matrix protein 1 GN=SRRM1 0.0161 GCN1L_HUMAN Translational activator GCN1 GN=GCN1L1 0.0211 Cluster of HSPB1_HUMAN Heat shock protein beta-1 GN=HSPB1 0.0234 Cluster of H0YI37_HUMAN ATP synthase subunit beta, mitochondrial (Fragment)

GN=ATP5B 0.0323

Cluster of M0R2B0_HUMAN rRNA 2'-O-methyltransferase fibrillarin (Fragment)

GN=FBL 0.0363

Cluster of CSDE1_HUMAN Isoform 4 of Cold shock domain-containing protein E1

GN=CSDE1 0.0369

Cluster of TADBP_HUMAN TAR DNA-binding protein 43 GN=TARDBP 0.0370 Cluster of RL27_HUMAN 60S ribosomal protein L27 GN=RPL27 0.0377 Cluster of RBM39_HUMAN RNA-binding protein 39 GN=RBM39 0.0379

Cluster of COF1_HUMAN Cofilin-1 GN=CFL1 0.0412

Cluster of SYYC_HUMAN Tyrosine--tRNA ligase, cytoplasmic GN=YARS 0.0445 E2AK2_HUMAN Interferon-induced, double-stranded RNA-activated protein

kinase GN=EIF2AK2 0.0448

FAS_HUMAN Fatty acid synthase GN=FASN 0.0449

Cluster of TFG_HUMAN Protein TFG GN=TFG 0.0468

Cluster of STRAP_HUMAN Serine-threonine kinase receptor-associated protein

GN=STRAP (Q9Y3F4) 0.0478

LARP4_HUMAN Isoform 5 of La-related protein 4 GN=LARP4 0.0482 Cluster of SYAC_HUMAN Alanine--tRNA ligase, cytoplasmic GN=AARS 0.0485 LMO4_HUMAN LIM domain transcription factor LMO4 GN=LMO4 0.0519 Cluster of HNRPL_HUMAN Heterogeneous nuclear ribonucleoprotein L

GN=HNRNPL 0.0532

RS10_HUMAN 40S ribosomal protein S10 GN=RPS10 0.0572

NARR_HUMAN Ras-related protein RAB34, isoform NARR GN=RAB34 0.0578

FSCN1_HUMAN Fascin GN=FSCN1 0.0716

Cluster of H0YDD8_HUMAN 60S acidic ribosomal protein P2 (Fragment)

GN=RPLP2 0.0732

Cluster of MCM7_HUMAN DNA replication licensing factor MCM7 GN=MCM7 0.0736

RL27A_HUMAN 60S ribosomal protein L27a GN=RPL27A 0.0759

Cluster of HNRPF_HUMAN Heterogeneous nuclear ribonucleoprotein F

GN=HNRNPF 0.0774

Cluster of HNRPK_HUMAN Heterogeneous nuclear ribonucleoprotein K

GN=HNRNPK 0.0782

Cluster of PFKAM_HUMAN ATP-dependent 6-phosphofructokinase, muscle type

GN=PFKM 0.0785

RL7A_HUMAN 60S ribosomal protein L7a GN=RPL7A 0.0814

Cluster of ECM29_HUMAN Proteasome-associated protein ECM29 homolog

GN=ECM29 0.0827

Cluster of D3DQV9_HUMAN Eukaryotic translation initiation factor 4 gamma 2

(Fragment) GN=EIF4G2 0.0853

KPRP_HUMAN Keratinocyte proline-rich protein GN=KPRP 0.0862 SND1_HUMAN Staphylococcal nuclease domain-containing protein 1 GN=SND1 0.0897 Cluster of ZCCHV_HUMAN Isoform 3 of Zinc finger CCCH-type antiviral protein 1

GN=ZC3HAV1 0.0947

Cluster of F5H5D3_HUMAN Tubulin alpha-1C chain GN=TUBA1C 0.0973 Cluster of HNRPQ_HUMAN Isoform 3 of Heterogeneous nuclear

ribonucleoprotein Q GN=SYNCRIP 0.0978

JAK1_HUMAN Tyrosine-protein kinase JAK1 GN=JAK1 0.1113

Cluster of B4DUR8_HUMAN T-complex protein 1 subunit gamma GN=CCT3 0.1129 Cluster of SRRM2_HUMAN Serine/arginine repetitive matrix protein 2

GN=SRRM2 0.1218

Cluster of ZNFX1_HUMAN NFX1-type zinc finger-containing protein 1 GN=ZNFX1 0.1499

DHX9_HUMAN ATP-dependent RNA helicase A GN=DHX9 0.1631

Cluster of SQSTM_HUMAN Sequestosome-1 GN=SQSTM1 0.1741

Cluster of MCTP2_HUMAN Multiple C2 and transmembrane domain-containing

protein 2 GN=MCTP2 0.1799

Cluster of H0YBN4_HUMAN Polyadenylate-binding protein 1 (Fragment)

GN=PABPC1 0.1889

Cluster of FXR2_HUMAN Fragile X mental retardation syndrome-related protein 2

GN=FXR2 0.2260

Cluster of RBP2_HUMAN E3 SUMO-protein ligase RanBP2 GN=RANBP2 0.3235 N.B. The t-test p-values are for a two tailed paired t-test without multiple testing correction. Yellow shading denotes proteins that were recorded in UNR samples only.