Machine Learning Discoveries of DNA Repair-X Synergy in ETC-1922159 Treated Colorectal Cancer Cells

Machine learning discoveries of DNA repair-X synergy in ETC-1922159 treated colorectal cancer cells shriprakash sinha Independent Researcher; Orcid ID : orcid.org/0000-0001-7027-5788 104-Madhurisha Heights Phase 1, Risali, Bhilai-490006, India Abstract Often, in biology, we are faced with the problem of exploring relevant unknown biological hypotheses in the form of myriads of combinations of factors/genes/proteins that might be affecting the pathway under certain conditions. In colorectal cancer (CRC) cells treated with ETC-1922159, many genes were found up and down regulated, individually. A recently developed search engine ranked combinations of DNA repair gene-X (X, a particular gene/protein) at 2nd order level after drug administration. These rankings reveal which Wnt-X combinations might be working synergistically in CRC. If found true, oncologists can further test the combination of interest in wet lab and determine the mechanism of functioning between the Wnt and X. In this research work, we cover combinations of RAD with X-ray repair cross complementing (XRCC) family, 5’-3’ exoribonuclease 2 (XRN2), NFKB repressing factor (NKRF), B cell CLL/lymphoma (BCL) family, exosome component (EXOSC) family, FA complementation group (FANC) family and XRCC with EXOSC. Keywords: DNA repair, Porcupine inhibitor ETC-1922159, Sensitivity analysis, Colorectal cancer. 1. Introduction In the unpublished preprint Sinha [1], a frame work of a search engine was developed which can rank combinations of factors (genes/proteins) in a signaling pathway. Such combinations are of import due to the vast search space in which they exist and the difficulty to find them. The search engine facilitates in prioritizing the combinations5 as ranked biological hypotheses which the biologists might want to test in wet lab, to know if a synergistic combination is prevalent in a signaling pathway, in a direct or indirect manner. Interested readers are advised to go through unpublished preprints IML dicoveries of DNA repair synergy in ETC-1922159 treated CRC cells Email address: [email protected] (shriprakash sinha) 1Aspects of unpublished work were presented in a poster session at (1) the recently concluded first ever Wnt Gordon Conference, from 6-11 August 2017, held in Stowe, VT 05672, USA. Preprint submitted to Preprint September 11, 2024 Sinha [1] and Sinha [2] for details regarding the search engine and the discoveries mentioned in there.10 2. Materials and Methods 2.1. Combinatorial search problem and a possible solution The issue of combinatorial search problem and a possible solution has been addressed in Sinha [3] and Sinha [2]. The details of the methodology of this manuscript have been explained in great detail in Sinha [3] & its application in Sinha [2]. Readers15 are requested to go through the same for gaining deeper insight into the working of the pipeline and its use of published data set generated after administration of ETC1922159. In order to understand the significance of the solution proposed to the problem of combinatorial search that the biologists face in revealing unknown biological search problem, these works are of importance.20 Briefly, from Sinha [2], the pipleline works by computing sensitivity indicies for each of these unique combinations and then vectorising these indices to connote and form discriminative feature vector for each combination. Since each combination is unique, the training and the test data are same. In the training data, the combinations are arranged and ranks from 1 to n are assigned. The ranking algorithm then learns25 the patterns from these combinations/sensitivity index vectors. Next the learned model is used to rank the test data by generating the ranking score for each of the unique combination. Sorting these shuffled scores of test data leads to prioritization of the combinations. Joachims [4] show an example of applying learned model to training data (same as the test data) in https://www.cs.cornell.edu/people/tj/svm_30 light/svm_rank.html. Note that these combinations are now ranked and give the biologists a chance to narrow down their focus on crucial biological hypotheses in the form of combinations which the biologists might want to test. Analogous to the webpage search engine, where the click of a button for a few key-words leads to a ranked list of web links, the pipeline uses sensitivity indices as an indicator of the strength of35 the influence of factors or their combinations, as a criteria to rank the combinations. 3. Results & Discussion 3.1. DNA repair related synergies 3.1.1. XRCC - RAD cross family analysis X-ray repair cross-complementing protein (XRCC) plays major role in DNA repair40 process, especially in Double Strand Repair (DBS) Thacker and Zdzienicka [5] and Thacker and Zdzienicka [6]. Sultana et al. [7] observe that ataxia telangiectasia mutated and RAD3 related (ATR) protein kinase inhibition is synthetically lethal in XRCC1 deficient ovarian cancer cells. Della-Maria et al. [8] observe that human Mre11/human RAD50/Nbs1 and DNA ligase IIIα/XRCC1 protein complexes act together in an al-45 ternative nonhomologous end joining pathway. These findings along with multiple 2 published work indicate the joint synergy of XRCC - RAD family. In colorectal cancer cell lines treated with ETC-1922159, both XRCC and RAD members were found to be down regulated. The search engine gave the 2nd order synergies between XRCC - RAD families, low numerical valued ranks to signify plausible synergistic down regulations50 that might not have been explored. Table 1 shows the rankings of RAD family w.r.t XRCC family and 2 shows the rankings of the XRCC family w.r.t RAD family. In table 1 we found RAD-18/51/51AP1/51C/54B/54L to be down regulated w.r.t XRCC1. These are reflected with rankings of 1027 (laplace), 456 (linear) and 1355 (rbf) for RAD-18 - XRCC1; 282 (laplace), 365 (linear) and 1003 (rbf) for RAD51 - XRCC1;55 753 (laplace), 5 (linear) and 27 (rbf) for RAD51AP1 - XRCC1; 337 (laplace), 111 (linear) and 968 (rbf) for RAD51C - XRCC1; 175 (laplace), 224 (linear) and 78 (rbf) for RAD54B - XRCC1; and 327 (laplace), 889 (linear) and 709 (rbf) for RAD54L - XRCC1. RAD-18/51/51AP1/51C/54B/54L were also found to be down regulated w.r.t XRCC2. These are reflected in 1388 (laplace), 847 (linear) and 765 (rbf) for60 XRCC2 - RAD18; 1247 (laplace), 1033 (linear) and 629 (rbf) for XRCC2 - RAD51; 302 (laplace); 247 (linear) and 42 (rbf) for XRCC2 - RAD51AP1; 1079 (laplace), 674 (linear) and 323 (rbf) for XRCC2 - RAD51C; 387 (laplace), 566 (linear) and 506 (rbf) for XRCC2 - RAD54B; and 976 (laplace), 918 (linear) and 847 (rbf) for XRCC2 - RAD54L. RAD-18/51/51AP1/51C/54B/54L were found to be down regulated with65 w.r.t XRCC6. These are reflected in 541 (laplace), 25 (linear) and 1068 (rbf) for RAD18 - XRCC6; 608 (laplace), 425 (linear) and 900 (rbf) for RAD51 - XRCC6; 216 (laplace), 67 (linear) and 83 (rbf) for RAD51AP1 - XRCC6; 426 (laplace), 865 (linear) and 503 (rbf) for RAD51C - XRCC6; 3 (laplace), 610 (linear) and 112 (rbf) for RAD54B - XRCC6; and 85 (laplace), 252 (linear) and 432 (rbf) for RAD54L70 - XRCC6. RAD-1/18/50/51/51AP1/51C/54B/54L were found to be down regulated w.r.t XRCC6BP1. These are reflected in 1167 (laplace) and 308 (rbf) for RAD1 - XRCC6BP1; 656 (linear) and 1612 (rbf) for RAD18 - XRCC6BP1; 1302 (laplace) and 328 (rbf) for XRCC6BP1 - RAD50; 435 (laplace), 495 (linear) and 1275 (rbf) for RAD51 - XRCC6BP1; 81 (laplace), 177 (linear) and 73 (rbf) for RAD51AP1 -75 XRCC6BP1; 645 (laplace), 1366 (linear) and 1414 (rbf) for RAD51C - XRCC6BP1; 154 (laplace), 693 (linear) and 1398 (rbf) for RAD54B - XRCC6BP1; and 420 (linear) and 1060 (rbf) for RAD54L - XRCC6BP1; In table 2 we found XRCC-2/6BP1 to be down regulated w.r.t RAD1. These are reflected in 62 (laplace), 498 (linear) and 1231 (rbf) for RAD1 - XRCC2; and 76480 (laplace) and 1325 (rbf) for RAD1 - XRCC6BP1. XRCC-1/2/6 were found to be down regulated with w.r.t RAD18. These are reflected in 927 (laplace) and 200 (rbf) for RAD18 - XRCC1; 506 (laplace) and 1517 (rbf) for RAD18 - XRCC2; and 279 (laplace) and 804 (rbf) for RAD18 - XRCC6; XRCC-2/6BP1 were found to be down regulated w.r.t RAD50. These are reflected in rankings of 53 (laplace), 244 (linear) and 147 (rbf)85 for XRCC-2 - RAD50; and 1375 (linear) and 1366 (rbf) for RAD50 - XRCC6BP1. XRCC-6/6BP1 were found to be down regulated w.r.t RAD51; These are reflected in rankings of 80 (laplace) and 1244 (linear) for XRCC6 - RAD51; and 792 (laplace), 951 (linear) and 1595 (rbf) for XRCC6BP1 - RAD51. XRCC-2/6BP1 were found to be down regulated w.r.t RAD51AP1. These were reflected in 78 (laplace), 11290 (linear) and 351 (rbf) for XRCC2 - RAD51AP1; and 936 (linear) and 974 (rbf) for XRCC6BP1 - RAD51AP1; XRCC2 was found to be down regulated w.r.t RAD51C. 3 RANKING RAD FAMILY W.R.TXRCC FAMILY RANKING OF RAD FAMILY W.R.TXRCC1 RANKING OF RAD FAMILY W.R.TXRCC2 laplace linear rbf laplace linear rbf RAD1 - XRCC1 1922 1658 1771 XRCC2 - RAD1 1921 893 1774 RAD18 - XRCC1 1027 456 1355 XRCC2 - RAD18 1388 847 765 XRCC1 - RAD50 2459 2254 2082 XRCC2 - RAD50 1877 2185 2546 RAD51 - XRCC1 282 365 1003 XRCC2 - RAD51 1247 1033 629 RAD51AP1 - XRCC1 753 5 275 XRCC2 - RAD51AP1 302 247 42 RAD51C - XRCC1 337 111 968 XRCC2 - RAD51C 1079 674 323 RAD54B - XRCC1 175 224 782 XRCC2 - RAD54B 387 566 506 RAD54L - XRCC1 327 889 709 XRCC2 - RAD54L 976 918 847 RANKING OF RAD FAMILY W.R.TXRCC6 RANKING OF RAD FAMILY W.R.TXRCC6BP1 laplace linear rbf laplace linear rbf XRCC6 - RAD1 1929 2029 2627 RAD1 - XRCC6BP1 1167 2417 308 RAD18 - XRCC6 541 25 1068 RAD18 - XRCC6BP1 656 1612 2271 XRCC6 - RAD50 2434 2043 2603 XRCC6BP1 - RAD50 1302 2263 328 RAD51 - XRCC6 608 425 900 RAD51 - XRCC6BP1 435 495 1275 RAD51AP1 - XRCC6 216 67 83 RAD51AP1 - XRCC6BP1 81 177 73 RAD51C - XRCC6 426 865 503 RAD51C - XRCC6BP1 645 1366 1414 RAD54B - XRCC6 3 610 112 RAD54B - XRCC6BP1 154 693 1398 RAD54L - XRCC6 85 252 432 RAD54L - XRCC6BP1 420 1060 2542 Table 1: 2nd order interaction ranking between RAD w.r.t XRCC family members. This are reflected in 1695 (laplace), 932 (linear) and 520 (rbf) for XRCC2 - RAD51C. XRCC2 was found to be down regulated w.r.t RAD54B. This is reflected in rankings of 1554 (laplace), 744 (linear) and 620 (rbf) for XRCC2 - RAD54B. XRCC-1/2/6/6BP195 were found to be down regulated w.r.t RAD54L. These are reflected in rankings of 657 (linear) and 525 (rbf) for XRCC1 - RAD54L; 167 (laplace) and 565 (rbf) for XRCC2 - RAD54L; 496 (linear) and 1247 (rbf) for XRCC6 - RAD54L; and 1389 (laplace), 1227 (linear) and 1454 (rbf) for RAD54L - XRCC6BP1; Table 3 shows the derived influences which can be represented graphically, with the100 following influences - •RAD w.r.t XRCC with RAD-18/51/51AP1/51C/54B/54L <− XRCC1; RAD-18/51/51AP1/51C/54B/54L <−XRCC2; RAD-18/51/51AP1/51C/54B/54L <−XRCC6 and RAD-1/18/50/51/51AP1/51C/54B/54L <−XRCC6BP1; •; XRCC w.r.t RAD with RAD1 −>XRCC-2/6BP1; RAD18 −>XRCC-1/2/6; RAD50 −> XRCC-2/6BP1; RAD51 −>XRCC-6/6BP1; RAD51AP1 −>XRCC-2/6BP1; RAD51C105 −>XRCC-2; RAD54B −>XRCC-2; RAD54L −>XRCC-1/2/6/6BP1; 4 RANKING XRCC FAMILY W.R.TRAD FAMILY RANKING OF XRCC W.R.TRAD1 RANKING OF XRCC W.R.TRAD18 laplace linear rbf laplace linear rbf RAD1 - XRCC1 1751 1808 793 RAD18 - XRCC1 927 2669 200 XRCC2 - RAD1 62 498 1231 XRCC2 - RAD18 506 1844 1517 XRCC6 - RAD1 2736 2511 1284 RAD18 - XRCC6 279 2193 804 RAD1 - XRCC6BP1 764 2108 1325 RAD18 - XRCC6BP1 819 1954 1976 RANKING OF XRCC W.R.TRAD50 RANKING OF XRCC W.R.TRAD51 laplace linear rbf laplace linear rbf XRCC1 - RAD50 2573 2374 2497 RAD51 - XRCC1 1673 1818 2611 XRCC2 - RAD50 53 244 147 XRCC2 - RAD51 472 2348 1973 XRCC6 - RAD50 2615 2568 2582 RAD51 - XRCC6 80 1244 2595 RAD50 - XRCC6BP1 1962 1375 1366 RAD51 - XRCC6BP1 792 951 1595 RANKING OF XRCC W.R.TRAD51AP1 RANKING OF XRCC W.R.TRAD51C laplace linear rbf laplace linear rbf XRCC1 - RAD51AP1 1802 2732 801 RAD51C - XRCC1 2282 1846 2026 XRCC2 - RAD51AP1 78 112 351 XRCC2 - RAD51C 1695 932 520 XRCC6 - RAD51AP1 2653 2439 347 RAD51C - XRCC6 2545 1848 1858 RAD51AP1 - XRCC6BP1 1790 936 974 RAD51C - XRCC6BP1 2325 1070 1844 RANKING OF XRCC W.R.TRAD54B RANKING OF XRCC W.R.TRAD54L laplace linear rbf laplace linear rbf XRCC1 - RAD54B 2475 2670 1824 RAD54L - XRCC1 1834 657 525 XRCC2 - RAD54B 1554 744 620 XRCC2 - RAD54L 2564 167 565 XRCC6 - RAD54B 2505 2709 2604 RAD54L - XRCC6 2597 496 1247 RAD54B - XRCC6BP1 1932 2504 2170 RAD54L - XRCC6BP1 1389 1227 1454 Table 2: 2nd order interaction ranking between XRCC w.r.t RAD family members. 5 UNEXPLORED COMBINATORIAL HYPOTHESES RAD w.r.t XRCC family RAD-18/51/51AP1/51C/54B/54L XRCC1 RAD-18/51/51AP1/51C/54B/54L XRCC2 RAD-18/51/51AP1/51C/54B/54L XRCC6 RAD-1/18/50/51/51AP1/51C/54B/54L XRCC6BP1 XRCC w.r.t RAD family RAD1 XRCC-2/6BP1 RAD18 XRCC-1/2/6 RAD50 XRCC-2/6BP1 RAD51 XRCC-6/6BP1 RAD51AP1 XRCC-2/6BP1 RAD51C XRCC-2 RAD54B XRCC-2 RAD54L XRCC-1/2/6/6BP1 Table 3: 2nd order combinatorial hypotheses between RAD and XRCC. 6 RANKING XRN2 W.R.TRAD FAMILY RANKING OF RAD FAMILY W.R.TXRN2 RANKING OF XRN2 W.R.TRAD FAMILY laplace linear rbf laplace linear rbf XRN2 - RAD51AP1 340 545 290 XRN2 - RAD51AP1 1905 1256 852 XRN2 - RAD51 387 560 605 XRN2 - RAD51 786 2647 1995 XRN2 - RAD54L 594 827 879 XRN2 - RAD54L 1541 1246 1819 XRN2 - RAD51C 639 1236 745 XRN2 - RAD51C 1037 1777 2228 XRN2 - RAD18 794 688 804 XRN2 - RAD18 904 2403 1801 XRN2 - RAD1 898 1955 2506 XRN2 - RAD1 255 122 2557 XRN2 - RAD54B 951 165 343 XRN2 - RAD54B 1818 2381 2603 XRN2 - RAD50 1330 2312 2295 XRN2 - RAD50 504 2100 1842 Table 4: 2nd order interaction ranking between RAD family vs XRN2. 3.1.2. XRN2 - RAD cross family analysis XRN2 (5’-3’ exoribonuclease 2) is involved in RNA synthesis/trafficking and termination. Morales et al. [9] observe that XRN2 links transcription termination to DNA damage and replication stress. They found an increase in the amount of RAD51 foci110 in shXRN2 cells compared to controls, suggesting that cells depleted of XRN2 are subjected to an increased level of basal DNA damage and show that loss of XRN2 also leads to the focal accumulation of several factors required for homologous recombination, such as ATM, BRCA1 and RAD51. This definitely shows that there is synergy between the XRN2 and RAD51. We found that both the XRN2 and RAD115 families were down regulated in CRC cell after ETC-1922159 treatment. The search engine gave rankings to the combinations of the XRN2 and RAD family members with low numerical valued in silico ranks. Table 4 shows the rankings of XRN2 w.r.t RAD family and vice versa. Following this is the derived influences in table 5. We find RAD-51AP1/51/54L/51C/18/54B to be down regulated w.r.t XRN2. These are re-120 flected in rankings of 340 (laplace), 545 (linear) and 290 (rbf) for RAD51AP1 - XRN2; 387 (laplace), 560 (linear) and 605 (rbf) for XRN2 - RAD51; 594 (laplace), 827 (linear) and 879 (rbf) for XRN2 - RAD54L; 639 (laplace), 1236 (linear) and 745 (rbf) for XRN2 - RAD51C; 794 (laplace), 688 (linear) and 804 (rbf) for XRN2 - RAD18; 255 (linear) and 122 (rbf) for XRN2 - RAD1 and 951 (laplace), 165 (linear) and 34125 (rbf) for XRN2 - RAD54B; On the other hand, XRN2 was found to be down regulated w.r.t RAD family. These are reflected in rankings of 255 (laplace) and 122 (rbf) for XRN2 - RAD1; 1256 (linear) and 852 (rbf) for XRN2 - RAD51AP1; 1541 (laplace) and 1246 (linear) for XRN2 - RAD54L and 1037 (laplace) and 1777 (linear) for XRN2 - RAD51C. Graphical depiction of XRN2 and RAD family dependencies is shown as130 •RAD w.r.t XRN2 with XRN2 −>RAD-51AP1/51/54L/51C/18/54B and •XRN2 w.r.t RAD with XRN2 <−RAD1; XRN2 <−RAD51AP1; XRN2 <−RAD54L; XRN2 <−RAD51C; Table 5 shows the derived influences which can be represented graphically, with the following influences - •RAD w.r.t XRN2 with XRN2 −>RAD-51AP1/51/54L/51C/18/54B;135 and •XRN2 w.r.t RAD with XRN2 <−RAD-1/51AP1/54L/51C. 7 UNEXPLORED COMBINATORIAL HYPOTHESES RAD w.r.t XRN2 XRN2 RAD-51AP1/51/54L/51C/18/54B XRN2 w.r.t RAD XRN2 RAD1 XRN2 RAD51AP1 XRN2 RAD54L XRN2 RAD51C Table 5: 2nd order combinatorial hypotheses between RAD and XRN2. 8 RANKING NKRF W.R.TRAD FAMILY RANKING OF NFRK W.R.TRAD FAMILY RANKING OF RAD FAMILY W.R.TNKRF laplace linear rbf laplace linear rbf RAD51AP1 - NKRF 1724 1642 649 RAD51AP1 - NKRF 157 553 2561 RAD51 - NKRF 982 1724 1352 RAD51 - NKRF 439 1441 1606 RAD54L - NKRF 1727 1387 1120 RAD54L - NKRF 117 1175 1415 RAD51C - NKRF 1568 472 1505 RAD51C - NKRF 418 2178 1653 RAD18 - NKRF 1508 615 405 RAD18 - NKRF 164 2306 1509 RAD1 - NKRF 2667 2222 1181 NKRF - RAD1 1391 1115 735 RAD54B - NKRF 1476 1189 1534 RAD54B - NKRF 207 1869 2244 RAD50 - NKRF 2003 2343 2511 NKRF - RAD50 1354 851 824 Table 6: 2nd order interaction ranking between RAD family vs NKRF. 3.1.3. NKRF - RAD cross family analysis Not much is known about the NKRF (NF-κB-repressing factor) and RAD members. We found the combinations to be down regulated by the search engine between NKRF and RAD family. Table 6 shows the rankings of NKRF and RAD family. We found140 NKRF down regulated w.r.t RAD family. These are reflected in rankings of 1724 (laplace), 1642 (linear) and 649 (rbf) for RAD51AP1 <−NKRF; 982 (laplace), 1724 (linear) and 1352 (rbf) RAD51 <−NKRF; 1727 (laplace), 1387 (linear) and 1120 (rbf) for RAD54L <−NKRF; 1568 (laplace), 472 (linear) and 1505 (rbf) for RAD51C <− NKRF; 1508 (laplace), 615 (linear) and 405 (rbf) for RAD18 <−NKRF; and 1476145 (laplace), 1189 (linear) and 1534 (rbf) for RAD54B <−NKRF; Also, we found RAD family to be down regulated w.r.t NKRF. These are reflected in rankings of 157 (laplace) and 553 (linear) for RAD51AP1 - NKRF; 439 (laplace), 1441 (linear) and 1606 (rbf) for RAD51 - NKRF; 117 (laplace), 1175 (linear) and 1415 (rbf) for RAD54L - NKRF; 418 (laplace), and 1653 (rbf) for RAD51C - NKRF; 164150 (laplace) and 1509 (rbf) for RAD18 - NKRF; 1391 (laplace), 1115 (linear) and 735 (rbf) NKRF - RAD1; 1354 (laplace), 851 (linear) and 824 (rbf) for NKRF - RAD50; Table 7 shows the derived influences which can be represented graphically, with the following influences - •RAD w.r.t NKRF with RAD51AP1 <−NKRF; RAD51 <−NKRF; RAD54L <−NKRF; RAD51C <−NKRF; RAD18 <−NKRF; RAD1155 <−NKRF; RAD54B <−NKRF and •NKRF w.r.t RAD with RAD51AP1 −> NKRF; RAD51 −>NKRF; RAD54L −>NKRF; RAD51C −>NKRF; RAD18 −>NKRF; NKRF −>RAD1; NKRF −>RAD50. 9 3.1.5. RAD - EXOSC cross family analysis Marin-Vicente et al. [12] show that RRP6/EXOSC10 is required for the repair of DNA double-strand breaks by homologous recombination. The authors results suggest that ribonucleolytic activity of RRP6/EXOSC10 is required for the recruitment of RAD51255 to DSBs. The therapeutic potential of exosome-mediated siRNA delivery was demonstrated in vitro by the strong knockdown of RAD51, a prospective therapeutic target for cancer cells (Shtam et al. [13]). These findings point to the synergy between EXOSC and RAD family. In CRC cells treated with ETC-1922159, they were down regulated and the search engine allocated low numerical rankings for combinations,260 thus pointing to possible synergistic down regulation. Table 10 shows the rankings of the EXOSC and RAD family w.r.t to each other. On the left half of the table is the rankings of EXOSC w.r.t RAD family. EXOSC2 was found to be down regulated w.r.t RAD-1/18/50/51/51AP1/51C/54B/54L. These are reflected in rankings of 1033 (laplace), 1311 (linear) and 1207 (rbf) for EXOSC2 - RAD1; 1210 (laplace) and 995265 (linear) for EXOSC2 - RAD18; 1124 (laplace), 698 (linear) and 629 (rbf) for EXOSC2 - RAD50; 1754 (laplace), 191 (linear)and 633 (rbf) and for EXOSC2 - RAD51; 198 (laplace) and 1462 (linear) for EXOSC2 - RAD51AP1; 87 (laplace), 463 (linear) and 1130 (rbf) for EXOSC2 - RAD51C; 351 (laplace), 135 (linear) and 142 (rbf) for EXOSC2 - RAD54B; and 1131 (laplace), 1652 (linear) and 320 (rbf) for EXOSC2 -270 RAD54L. EXOSC3 was found to be down regulated w.r.t RAD-1/18/51/51AP1/54L. These are reflected in rankings of 1677 (linear) and 549 (rbf) for EXOSC3 - RAD1; 1676 (laplace) and 184 (rbf) for EXOSC3 - RAD18; 894 (laplace) and 1066 (linear) for EXOSC3 - RAD51; 1037 (linear) and 804 (rbf) for EXOSC3 - RAD51AP1, and 469 (linear) and 736 (rbf) for EXOSC3 - RAD54L. EXOSC5 was found to be down275 regulated w.r.t RAD-1/18/50/51/51AP1/51C/54B/54L. These are reflected in rankings of 568 (laplace), 1169 (linear) and 1699 (rbf) for EXOSC5 - RAD1; 219 (linear) and 1652 (rbf) for EXOSC5 - RAD18; 447 (laplace), 195 (linear) and 475 (rbf) for EXOSC5 - RAD50; 431 (linear) and 1121 (rbf) for EXOSC5 - RAD51; 1290 (laplace), 487 (linear) and 430 (rbf) for EXOSC5 - RAD51AP1; 1284 (laplace) and 1264 (lin-280 ear) for EXOSC5 - RAD51C; 940 (laplace), 812 (linear) and 1036 (rbf) for EXOSC5 - RAD54B; and 408 (laplace) and 1407 (rbf) for EXOSC5 - RAD54L; EXOSC6 was found to be down regulated w.r.t RAD-18/51/54L. These were reflected in rankings of 1637 (laplace), 1599 (linear) and 2254 (rbf) for EXOSC6 - RAD18; 1056 (laplace), 1482 (linear) and 1007 (rbf) for EXOSC6 - RAD51; and 987 (laplace) and 1642285 (rbf) for EXOSC6 - RAD54L; EXOSC7 was found to be down regulated w.r.t RAD1/18/51C/54B/54L. These are reflected in rankings of 1735 (linear) and 1210 (rbf) for EXOSC7 - RAD1; 490 (laplace), 1688 (linear) and 1331 (rbf) for EXOSC7 - RAD18; 1113 (laplace), 1623 (linear) and 530 (rbf) for EXOSC7 - RAD51C; 1612 (linear) and 1191 (rbf) for EXOSC7 - RAD54B; and 1550 (laplace), 1754 (linear) and 1728290 (rbf) for EXOSC7 - RAD54L; EXOSC8 was found to be down regulated w.r.t RAD18/51/51AP1/54B/54L. These are reflected in 805 (laplace) and 1564 (rbf) for EXOSC8 - RAD18; 404 (laplace) and 1630 (linear) for EXOSC8 - RAD51; 1567 (linear) and 1701 (rbf) for EXOSC8 - RAD51AP1; 1562 (laplace) and 1736 (rbf) for EXOSC8 - RAD54B; and 1248 (laplace), 622 (linear) and 239 (rbf) for EXOSC8 - RAD54L;295 EXOSC9 was found to be down regulated w.r.t RAD-1/18/50/51/51C/54B/54L. These 16 are reflected in rankings of 175 (linear) and 1648 (rbf) for EXOSC9 - RAD1; 1533 (laplace), 774 (linear) and 1180 (rbf) for EXOSC9 - RAD18; 545 (laplace), 183 (linear) and 467 (rbf) for EXOSC9 - RAD50; 866 (laplace), 106 (linear) and 99 (rbf) for EXOSC9 - RAD51; 110 (laplace), 742 (linear) and 200 (rbf) for EXOSC9 - RAD51C;300 179 (laplace), 178 (linear) and 84 (rbf) for EXOSC9 - RAD54B and 1113 (laplace) and 22 (rbf) for EXOSC9 - RAD54L; On the right half of the table is the rankings of RAD family w.r.t EXOSC. RAD18/51/51C/54B/54L was found to be down regulated w.r.t EXOSC2. These are reflected in rankings of 1115 (laplace), 979 (linear) and 654(rbf) for EXOSC2 - RAD18;305 795 (laplace), 1332 (linear) and 441(rbf) for EXOSC2 - RAD51; 636 (laplace), 564 (linear) and 152(rbf) for EXOSC2 - RAD51C; 278 (laplace), 132 (linear) and 282(rbf) for EXOSC2 - RAD54B and 125 (laplace), 888 (linear) and 545(rbf) for EXOSC2 - RAD54L. RAD-18/50/51/51AP1/51C/54B/54L was found to be down regulated w.r.t EXOSC3. These are reflected in rankings of 1468 (linear) and 767 (rbf) for EXOSC3310 - RAD18; 1062 (laplace) and 596 (linear) for EXOSC3 - RAD50; 727 (laplace), 583 (linear) and 963 (rbf) for EXOSC3 - RAD51; 100 (laplace), 49 (linear) and 219 (rbf) for EXOSC3 - RAD51AP1; 663 (laplace), 869 (linear) and 887 (rbf) for EXOSC3 - RAD51C; 384 (laplace), 277 (linear) and 310 (rbf) for EXOSC3 - RAD54B and 546 (laplace), 1117 (linear) and 808 (rbf) for EXOSC3 - RAD54L; RAD-1/18/51/51AP1/51C/54B/54L315 was found to be down regulated w.r.t EXOSC5. These are reflected in rankings of 1716 (linear) and 1718 (rbf) for EXOSC5 - RAD1; 1026 (laplace), 550 (linear) and 253 (rbf) for EXOSC5 - RAD18; 260 (laplace), 1095 (linear) and 137 (rbf) for EXOSC5 - RAD51; 1555 (laplace) and 976 (rbf) for EXOSC5 - RAD51AP1; 233 (laplace), 1003 (linear) and 359 (rbf) for EXOSC5 - RAD51C; 834 (laplace), 1825 (linear)320 and 335 (rbf) for EXOSC5 - RAD54B; and 248 (laplace), 197 (linear) and 39 (rbf) for EXOSC5 - RAD54L. RAD-1/18/50/51AP1/51C/54L was found to be down regulated w.r.t EXOSC6. These are reflected in rankings of 142 (linear) and 639(rbf) for EXOSC6 - RAD1; 1118 (laplace), 1313 (linear) and 1549(rbf) for EXOSC6 - RAD18; 1722 (linear) and 575(rbf) for EXOSC6 - RAD50; 149 (laplace) and 1060325 (linear) for EXOSC6 - RAD51AP1; 500 (laplace) and 1628 (linear) for EXOSC6 - RAD51C; and 885 (laplace), 271 (linear) and 1224(rbf) for EXOSC6 - RAD54L; RAD-18/51/51AP1/51C/54B/54L was found to be down regulated w.r.t EXOSC7. These were reflected in rankings of 441 (laplace), 385 (linear) and 1542(rbf) for EXOSC7 - RAD18; 376 (laplace), 1180 (linear) and 550(rbf) for EXOSC7 - RAD51; 35330 (laplace), 97 (linear) and 786(rbf) for EXOSC7 - RAD51AP1; 854 (laplace), 671 (linear) and 1459(rbf) for EXOSC7 - RAD51C; 458 (laplace), 260 (linear) and 646(rbf) for EXOSC7 - RAD54B; and 464 (laplace), 528 (linear) and 790(rbf) for EXOSC7 - RAD54L; RAD-1/18/51/51AP1/51C/54B/54L was found to be down regulated w.r.t EXOSC8. These were reflected in rankings of 151 (linear) and 1563 (rbf) for EXOSC8335 - RAD1; 764 (laplace), 523 (linear) and 29 (rbf) for EXOSC8 - RAD18; 98 (laplace), 1161 (linear) and 902 (rbf) for EXOSC8 - RAD51; 408 (laplace) and 541 (rbf) for EXOSC8 - RAD51AP1; 906 (laplace), 738 (linear) and 1052 (rbf) for EXOSC8 - RAD51C; 23 (laplace), 1578 (linear) and 130 (rbf) for EXOSC8 - RAD54B; and 651 (laplace), 1384 (linear) and 1047 (rbf) for EXOSC8 - RAD54L; RAD-1/18/50/51/51AP1/51C/54B/54L340 was found to be down regulated w.r.t EXOSC9. These were reflected in rankings of 1335 (laplace) and 978 (rbf) for EXOSC9 - RAD1; 54 (linear) and 540 (rbf) for EX17 OSC9 - RAD18; 211 (laplace) and 1377 (rbf) for EXOSC9 - RAD50; 807 (laplace), 74 (linear) and 429 (rbf) for EXOSC9 - RAD51; 103 (linear), 1210 (rbf) for EXOSC9 - RAD51AP1; 399 (laplace), 844 (linear) and 69 (rbf) for EXOSC9 - RAD51C; 466345 (linear), 1286 (rbf) for EXOSC9 - RAD54B; and 536 (laplace), 724 (linear) and 414 (rbf) for EXOSC9 - RAD54L; Table 11 shows the derived influences which can be represented graphically, with the following influences - •RAD w.r.t EXOSC with EXOSC-2 −>RAD-18/51/51C/54B/54L; EXOSC-3 −>RAD-18/50/51/51AP1/51C/54B/54L; EXOSC-5 −>RAD-1/18/51/51AP1/51C/54B/54L;350 EXOSC-6 −>RAD-1/18/50/51AP1/51C/54L; EXOSC-7 −>RAD-18/51/51AP1/51C/54B/54L; EXOSC-8 −>RAD-1/18/51/51AP1/51C/54B/54L; EXOSC-9 −>RAD-1/18/50/51/51AP1/51C/54B/54L; and •EXOSC w.r.t RAD with EXOSC-2 <−RAD-1/18/50/51/51AP1/51C/54B/54L; EXOSC-3 <−RAD-1/18/51/51AP1/54L; EXOSC-5 <−RAD-1/18/50/51/51AP1/51C/54B/54L; EXOSC-6 <−RAD-18/51/54L; EXOSC-7 <−RAD-1/18/51C/54B/54L; EXOSC-8355 <−RAD-18/51/51AP1/54B/54L; and EXOSC-9 <−RAD-1/18/50/51/51C/54B/54L. 18 RANKING RAD FAMILY VS EXOSC FAMILY RANKING OF EXOSC2 W.R.TRAD FAMILY RANKING OF RAD FAMILY W.R.TEXOSC2 laplace linear rbf laplace linear rbf EXOSC2 - RAD1 1033 1311 1207 EXOSC2 - RAD1 2456 1368 2292 EXOSC2 - RAD18 1210 995 1906 EXOSC2 - RAD18 1115 979 654 EXOSC2 - RAD50 1124 698 629 EXOSC2 - RAD50 1647 2495 2375 EXOSC2 - RAD51 1754 191 633 EXOSC2 - RAD51 795 1332 441 EXOSC2 - RAD51AP1 198 1462 2718 EXOSC2 - RAD51AP1 2320 1316 2127 EXOSC2 - RAD51C 87 463 1130 EXOSC2 - RAD51C 636 564 152 EXOSC2 - RAD54B 351 135 142 EXOSC2 - RAD54B 278 132 282 EXOSC2 - RAD54L 1131 1652 320 EXOSC2 - RAD54L 125 888 545 RANKING OF EXOSC3 W.R.TRAD FAMILY RANKING OF RAD FAMILY W.R.TEXOSC3 laplace linear rbf laplace linear rbf EXOSC3 - RAD1 2492 1677 549 EXOSC3 - RAD1 2200 1243 2711 EXOSC3 - RAD18 1676 2516 184 EXOSC3 - RAD18 2024 1468 767 EXOSC3 - RAD50 2368 1892 2204 EXOSC3 - RAD50 1062 596 2346 EXOSC3 - RAD51 894 1066 2463 EXOSC3 - RAD51 727 583 963 EXOSC3 - RAD51AP1 1884 1037 804 EXOSC3 - RAD51AP1 100 49 219 EXOSC3 - RAD51C 2499 2356 1248 EXOSC3 - RAD51C 663 869 887 EXOSC3 - RAD54B 2183 2518 2360 EXOSC3 - RAD54B 384 277 310 EXOSC3 - RAD54L 1735 469 736 EXOSC3 - RAD54L 546 1117 808 RANKING OF EXOSC5 W.R.TRAD FAMILY RANKING OF RAD FAMILY W.R.TEXOSC5 laplace linear rbf laplace linear rbf EXOSC5 - RAD1 568 1169 1699 EXOSC5 - RAD1 2405 1716 1718 EXOSC5 - RAD18 2481 219 1652 EXOSC5 - RAD18 1026 550 253 EXOSC5 - RAD50 447 195 475 EXOSC5 - RAD50 1596 1952 2271 EXOSC5 - RAD51 2548 431 1121 EXOSC5 - RAD51 260 1095 137 EXOSC5 - RAD51AP1 1290 487 430 EXOSC5 - RAD51AP1 1555 1860 976 EXOSC5 - RAD51C 1284 1264 1790 EXOSC5 - RAD51C 233 1003 359 EXOSC5 - RAD54B 940 812 1036 EXOSC5 - RAD54B 834 1825 335 EXOSC5 - RAD54L 408 2539 1407 EXOSC5 - RAD54L 248 197 39 RANKING OF EXOSC6 W.R.TRAD FAMILY RANKING OF RAD FAMILY W.R.TEXOSC6 laplace linear rbf laplace linear rbf EXOSC6 - RAD1 2283 2490 1228 EXOSC6 - RAD1 2405 142 639 EXOSC6 - RAD18 1637 1599 2254 EXOSC6 - RAD18 1118 1313 1549 EXOSC6 - RAD50 2289 1969 1797 EXOSC6 - RAD50 2309 1722 575 EXOSC6 - RAD51 1056 1482 1007 EXOSC6 - RAD51 998 2297 2219 EXOSC6 - RAD51AP1 1854 2480 1827 EXOSC6 - RAD51AP1 149 1060 2731 EXOSC6 - RAD51C 1996 940 1842 EXOSC6 - RAD51C 500 1628 2409 EXOSC6 - RAD54B 2289 2312 2005 EXOSC6 - RAD54B 262 2703 2465 EXOSC6 - RAD54L 987 2240 1642 EXOSC6 - RAD54L 885 271 1224 RANKING OF EXOSC7 W.R.TRAD FAMILY RANKING OF RAD FAMILY W.R.TEXOSC7 laplace linear rbf laplace linear rbf EXOSC7 - RAD1 2559 1735 1210 EXOSC7 - RAD1 2079 2308 1604 EXOSC7 - RAD18 490 1688 1331 EXOSC7 - RAD18 441 385 1542 EXOSC7 - RAD50 2661 1939 2021 EXOSC7 - RAD50 1840 406 2100 EXOSC7 - RAD51 842 1900 1876 EXOSC7 - RAD51 376 1180 550 EXOSC7 - RAD51AP1 2446 349 2374 EXOSC7 - RAD51AP1 35 97 786 EXOSC7 - RAD51C 1113 1623 530 EXOSC7 - RAD51C 854 671 1459 EXOSC7 - RAD54B 2431 1612 1191 EXOSC7 - RAD54B 458 260 646 EXOSC7 - RAD54L 1550 1754 1728 EXOSC7 - RAD54L 464 528 790 RANKING OF EXOSC8 W.R.TRAD FAMILY RANKING OF RAD FAMILY W.R.TEXOSC8 laplace linear rbf laplace linear rbf EXOSC8 - RAD1 2380 2442 2630 EXOSC8 - RAD1 1928 151 1563 EXOSC8 - RAD18 805 2287 1564 EXOSC8 - RAD18 764 523 29 EXOSC8 - RAD50 1798 1830 1893 EXOSC8 - RAD50 2103 2649 1822 EXOSC8 - RAD51 404 1630 2092 EXOSC8 - RAD51 98 1161 902 EXOSC8 - RAD51AP1 1932 1567 1701 EXOSC8 - RAD51AP1 408 1824 541 EXOSC8 - RAD51C 2439 1576 2554 EXOSC8 - RAD51C 906 738 1052 EXOSC8 - RAD54B 1562 2542 1736 EXOSC8 - RAD54B 23 1578 130 EXOSC8 - RAD54L 1248 622 239 EXOSC8 - RAD54L 651 1384 1047 RANKING OF EXOSC9 W.R.TRAD FAMILY RANKING OF RAD FAMILY W.R.TEXOSC9 laplace linear rbf laplace linear rbf EXOSC9 - RAD1 2240 175 1648 EXOSC9 - RAD1 1335 1799 978 EXOSC9 - RAD18 1533 774 1180 EXOSC9 - RAD18 2529 54 540 EXOSC9 - RAD50 545 183 467 EXOSC9 - RAD50 211 2217 1377 EXOSC9 - RAD51 866 106 99 EXOSC9 - RAD51 807 74 429 EXOSC9 - RAD51AP1 1570 1819 1807 EXOSC9 - RAD51AP1 2480 103 1210 EXOSC9 - RAD51C 110 742 200 EXOSC9 - RAD51C 399 844 69 EXOSC9 - RAD54B 179 178 84 EXOSC9 - RAD54B 2385 466 1286 EXOSC9 - RAD54L 1113 2436 22 EXOSC9 - RAD54L 536 724 414 Table 10: 2nd order interaction ranking between RAD and EXOSC family members. 19 UNEXPLORED COMBINATORIAL HYPOTHESES RAD w.r.t EXOSC EXOSC-2 RAD-18/51/51C/54B/54L EXOSC-3 RAD-18/50/51/51AP1/51C/54B/54L EXOSC-5 RAD-1/18/51/51AP1/51C/54B/54L EXOSC-6 RAD-1/18/50/51AP1/51C/54L EXOSC-7 RAD-18/51/51AP1/51C/54B/54L EXOSC-8 RAD-1/18/51/51AP1/51C/54B/54L EXOSC-9 RAD-1/18/50/51/51AP1/51C/54B/54L EXOSC w.r.t RAD EXOSC-2 RAD-1/18/50/51/51AP1/51C/54B/54L EXOSC-3 RAD-1/18/51/51AP1/54L EXOSC-5 RAD-1/18/50/51/51AP1/51C/54B/54L EXOSC-6 RAD-18/51/54L EXOSC-7 RAD-1/18/51C/54B/54L EXOSC-8 RAD-18/51/51AP1/54B/54L EXOSC-9 RAD-1/18/50/51/51C/54B/54L Table 11: 2nd order combinatorial hypotheses between RAD and EXOSC members. 20 3.1.6. XRCC - EXOSC cross family analysis Not much is known about XRCC - EXOSC synergy, however both were found to be down regulated in CRC cells after treatment with ETC-1922159. The search engine also allocated rankings of low numerical values to several combinations thus indicat-360 ing plausible synergistic down regulations. Table 12 shows the rankings of XRCC vs EXOSC family members. On the left half of the table is the rankings of EXOSC w.r.t XRCC family. EXOSC2 was found to be down regulated w.r.t XRCC-1/2/6/6BP1. These are reflected in rankings of 277 (laplace), 176 (linear) and 423 (rbf) for EXOSC2 - XRCC1; 8 (laplace), 38365 (linear) and 100 (rbf) for EXOSC2 - XRCC2; 1252 (laplace), 398 (linear) and 623 (rbf) for EXOSC2 - XRCC6; and 935 (laplace) and 905 (linear) for EXOSC2 - XRCC6BP1; EXOSC3 was found to be down regulated w.r.t XRCC-6BP1. These are reflected in rankings of 1523 (linear) and 1356 (rbf) for EXOSC3 - XRCC6BP1; EXOSC5 was found to be down regulated w.r.t XRCC-1/2/6/6BP1. These are reflected in rankings370 of 741 (laplace), 291 (linear) and 8 (rbf) for EXOSC5 - XRCC1; 1244 (laplace), 791 (linear) and 702 (rbf) for EXOSC5 - XRCC2; 65 (laplace), 1064 (linear) and 322 (rbf) for EXOSC5 - XRCC6; and 416 (laplace), 880 (linear) and 1434 (rbf) for EXOSC5 - XRCC6BP1. EXOSC6 was found to be down regulated w.r.t XRCC-1/2. These are reflected in rankings of 985 (linear) and 1163 (rbf) for EXOSC6 - XRCC1 and 1512375 (laplace), 648 (linear) and 1458 (rbf) for EXOSC6 - XRCC2; EXOSC7 was found to be down regulated w.r.t XRCC-1/6/6BP1. These are reflected in rankings of 1510 (linear) and 1603 (rbf) for EXOSC7 - XRCC1; 584 (laplace), 1523 (linear) and 1018 (rbf) for EXOSC7 - XRCC6; and 1419 (laplace) and 876 (rbf) for EXOSC7 - XRCC6BP1. EXOSC8 was found to be down regulated w.r.t XRCC-1. These are reflected in rank-380 ings of 1373 (laplace) and 1515 (linear) for EXOSC8 - XRCC1; EXOSC9 was found to be down regulated w.r.t XRCC-1/2/6/6BP1. These are reflected in rankings of 44 (laplace), 1214 (linear) and 1410 (rbf) for EXOSC9 - XRCC1; 496 (laplace), 672 (linear) and 840 (rbf) for EXOSC9 - XRCC2; 1121 (laplace), 151 (linear) and 689 (rbf) for EXOSC9 - XRCC6 and 362 (laplace), 463 (linear) and 1741 (rbf) for EXOSC9 -385 XRCC6BP1. On the right half of the table is the rankings of XRCC w.r.t EXOSC family. W.r.t EXOSC2, XRCC-2 was found to be down regulated. These are reflected in rankings of 166 (laplace), 417 (linear) and 56 (rbf) for EXOSC2 - XRCC2. W.r.t W.r.t EXOSC3, XRCC-2 was found to be down regulated. These are reflected in rankings of 166390 (laplace), 417 (linear) and 56 (rbf) for EXOSC3 - XRCC2. W.r.t EXOSC5, XRCC2 was found to be down regulated. These are reflected in rankings of 1559 (laplace) and 56 (rbf) for EXOSC5 - XRCC2. W.r.t EXOSC6, XRCC-1/2/6/6BP1 were found to be down regulated. These are reflected in rankings of 509 (laplace) and 1046(rbf) for EXOSC6 - XRCC1; 486 (laplace) and 1901(rbf) for EXOSC6 - XRCC2; 35 (lin-395 ear) and 188(rbf) for EXOSC6 - XRCC6; 1295 (linear) and 366 (rbf) for EXOSC6 - XRCC6BP1. W.r.t EXOSC7, XRCC-6 was found to be down regulated. These are reflected in rankings of 1229 (linear) and 987(rbf) for EXOSC7 - XRCC1; 176 (laplace), 436 (linear) and 788 (rbf) for EXOSC7 - XRCC2; and 1074 (laplace), 242 (linear) and 288(rbf) for EXOSC7 - XRCC6. W.r.t EXOSC8, XRCC-2 was found to be down400 regulated. These are reflected in rankings of 13 (laplace) and 6 (rbf) for EXOSC8 - 21 RANKING XRCC FAMILY VS EXOSC FAMILY RANKING OF EXOSC2 W.R.TXRCC FAMILY RANKING OF XRCC FAMILY W.R.TEXOSC2 laplace linear rbf laplace linear rbf EXOSC2 - XRCC1 277 176 423 EXOSC2 - XRCC1 2708 2386 2634 EXOSC2 - XRCC2 8 38 100 EXOSC2 - XRCC2 166 417 56 EXOSC2 - XRCC6 1252 398 623 EXOSC2 - XRCC6 2678 2504 2576 EXOSC2 - XRCC6BP1 935 905 1755 EXOSC2 - XRCC6BP1 1740 1842 2177 RANKING OF EXOSC3 W.R.TXRCC FAMILY RANKING OF XRCC FAMILY W.R.TEXOSC3 laplace linear rbf laplace linear rbf EXOSC3 - XRCC1 1551 2256 1974 EXOSC3 - XRCC1 2217 1418 2041 EXOSC3 - XRCC2 2462 2553 2329 EXOSC3 - XRCC2 125 15 194 EXOSC3 - XRCC6 1720 1716 2398 EXOSC3 - XRCC6 2742 2608 2193 EXOSC3 - XRCC6BP1 2506 1523 1356 EXOSC3 - XRCC6BP1 2561 2154 2406 RANKING OF EXOSC5 W.R.TXRCC FAMILY RANKING OF XRCC FAMILY W.R.TEXOSC5 laplace linear rbf laplace linear rbf EXOSC5 - XRCC1 741 291 8 EXOSC5 - XRCC1 2578 2568 1910 EXOSC5 - XRCC2 1244 791 702 EXOSC5 - XRCC2 1559 1857 866 EXOSC5 - XRCC6 65 1064 322 EXOSC5 - XRCC6 2410 2465 2190 EXOSC5 - XRCC6BP1 416 880 1434 EXOSC5 - XRCC6BP1 1907 2029 1394 RANKING OF EXOSC6 W.R.TXRCC FAMILY RANKING OF XRCC FAMILY W.R.TEXOSC6 laplace linear rbf laplace linear rbf EXOSC6 - XRCC1 1890 985 1163 EXOSC6 - XRCC1 509 2373 1046 EXOSC6 - XRCC2 1512 648 1458 EXOSC6 - XRCC2 486 2564 1901 EXOSC6 - XRCC6 2304 1719 2690 EXOSC6 - XRCC6 2576 35 188 EXOSC6 - XRCC6BP1 2428 492 2112 EXOSC6 - XRCC6BP1 1753 1295 366 RANKING OF EXOSC7 W.R.TXRCC FAMILY RANKING OF XRCC FAMILY W.R.TEXOSC7 laplace linear rbf laplace linear rbf EXOSC7 - XRCC1 1907 1510 1603 EXOSC7 - XRCC1 1844 1229 987 EXOSC7 - XRCC2 1369 2555 2124 EXOSC7 - XRCC2 176 436 788 EXOSC7 - XRCC6 584 1523 1018 EXOSC7 - XRCC6 1074 242 288 EXOSC7 - XRCC6BP1 1419 1944 876 EXOSC7 - XRCC6BP1 2144 1577 2038 RANKING OF EXOSC8 W.R.TXRCC FAMILY RANKING OF XRCC FAMILY W.R.TEXOSC8 laplace linear rbf laplace linear rbf EXOSC8 - XRCC1 1373 1515 2103 EXOSC8 - XRCC1 1769 2151 1435 EXOSC8 - XRCC2 1086 2309 2435 EXOSC8 - XRCC2 13 1932 6 EXOSC8 - XRCC6 1820 2542 2693 EXOSC8 - XRCC6 1869 1233 2625 EXOSC8 - XRCC6BP1 2112 1994 2699 EXOSC8 - XRCC6BP1 2305 2461 2319 RANKING OF EXOSC9 W.R.TXRCC FAMILY RANKING OF XRCC FAMILY W.R.TEXOSC9 laplace linear rbf laplace linear rbf EXOSC9 - XRCC1 44 1214 1410 EXOSC9 - XRCC1 1804 2696 1629 EXOSC9 - XRCC2 496 672 840 EXOSC9 - XRCC2 1793 655 1526 EXOSC9 - XRCC6 1121 151 689 EXOSC9 - XRCC6 1882 2188 2404 EXOSC9 - XRCC6BP1 362 463 1741 EXOSC9 - XRCC6BP1 1206 1776 1626 Table 12: 2nd order interaction ranking between RAD and EXOSC family members. XRCC2. W.r.t EXOSC9, XRCC-2 was found to be down regulated. These are reflected in rankings of 655 (linear) and 1526 (rbf) for EXOSC9 - XRCC2 and 1206 (laplace) and 1626 (rbf) for EXOSC9 - XRCC6BP1; Table 13 shows the derived influences which can be represented graphically, with405 the following influences - •XRCC w.r.t EXOSC with EXOSC-2 −>XRCC-2; EXOSC3−>XRCC-2; EXOSC-5 −>XRCC-2; EXOSC-6 −>XRCC-6; EXOSC-7 −> 22 UNEXPLORED COMBINATORIAL HYPOTHESES XRCC w.r.t EXOSC EXOSC-2 XRCC-2 EXOSC-3 XRCC-2 EXOSC-5 XRCC-2 EXOSC-6 XRCC-6 EXOSC-7 XRCC-1/2/6 EXOSC-8 XRCC-2 EXOSC-9 XRCC-2/6BP1 EXOSC w.r.t XRCC EXOSC-2 XRCC-1/2/6/6BP1 EXOSC-3 XRCC-6/6BP1 EXOSC-5 XRCC-1/2/6/6BP1 EXOSC-6 XRCC-1/2 EXOSC-7 XRCC-1/6/6BP1 EXOSC-8 XRCC-1 EXOSC-9 XRCC-1/2/6/6BP1 Table 13: 2nd order combinatorial hypotheses between XRCC and EXOSC members. 23 XRCC-1/2/6; EXOSC-8 −>XRCC-2; EXOSC-9 −>XRCC-2/6BP1; and •EXOSC w.r.t XRCC with EXOSC-2 <−XRCC-1/2/6/6BP1; EXOSC-3 <−XRCC-6/6BP1; EXOSC-5 <−XRCC-1/2/6/6BP1; EXOSC-6 <−XRCC-1/2; EXOSC-7 ¡- XRCC-410 1/6/6BP1; EXOSC-8 <−XRCC-1; and EXOSC-9 <−XRCC-1/2/6/6BP1. 24 3.1.7. RAD - FANC cross family analysis Fanconi Anemia (FA) is rare genetic disorder that happens mainly due to defects in proteins responsible for DNA repair via homologous recombination (Walden and Deans [14]). Cohn and D’Andrea [15] provides a review on the recent discoveries in the415 Fanconi Anemia and DNA double-strand break (DSB) repair pathways, which underscore the importance of regulated chromatin loading in the DNA damage response. Romick-Rosendale et al. [16] study the role Fanconi anemia pathway in squamous Cell Carcinoma. A review of the interplay between Fanconi anemia and homologous recombination pathways in genome integrity has been conducted by Michl et al. [17].420 Liang et al. [18] observe the role of trimeric RAD51 and RAD51AP1-UAF1 complex in FANCD2. Taniguchi et al. [19] observe S-phase-specific interaction of the Fanconi anemia protein, FANCD2, with BRCA1 and RAD51. Zadorozhny et al. [20] show Fanconi anemia associated mutations destabilize RAD51 filaments and impair replication fork protection. Geng et al. [21] find RAD18-mediated ubiquitination of PCNA425 activates the Fanconi anemia DNA repair network. Rad18 E3 ubiquitin ligase activity mediates Fanconi anemia pathway activation and cell survival following DNA topoisomerase 1 inhibition as shown by Palle and Vaziri [22]. Garc´ ıa-Luis and Mach´ ın [23] observe that Fanconi anaemia-like Mph1 helicase backs up RAD54 and RAD5 to circumvent replication stress-driven chromosome bridges. These findings suggest deep430 interactive role between the RAD and FA family. In colorectal cancer cell treated with ETC-1922159 these were found to both families were found to be down regulated. Our search engine alloted low laved numerical ranks to many of the 2nd order combinations between the RAD - FANC family. This signifies possible synergistic mechanism between the two in CRC cells. Table 15 shows the rankings of each, with respect to the435 other. On the left half is the rankings of RAD family w.r.t FANC family and vice versa on the right half. On the left half, we find, RAD-18/51/51AP1/51C/54B/54L were found to be down regulated w.r.t FANCB. These are reflected in rankings of 10 (laplace), 2219 (linear) and 625 (rbf) for RAD18 - FANCB; 247 (laplace), 73 (linear) and 610 (rbf) for RAD51440 - FANCB; 479 (laplace), 1667 (linear) and 663 (rbf) for RAD51AP1 - FANCB; 769 (laplace), 536 (linear) and 887 (rbf) for RAD51C - FANCB; 468 (laplace), 133 (linear) and 438 (rbf) for RAD54B - FANCB; and 583 (laplace), 2131 (linear) and 160 (rbf) for RAD54L - FANCB. RAD-18/51/51AP1/54B/54L were found to be down regulated w.r.t FANCD2. These are reflected in rankings of 1035 (laplace), 1271 (linear) and445 405 (rbf) for RAD18 - FANCD2; 885 (laplace) and 1383 (rbf) for RAD51 - FANCD2; 1734 (laplace), 644 (linear) and 1291 (rbf) for RAD51AP1 - FANCD2; 275 (laplace), 2460 (linear) and 478 (rbf) for RAD54B - FANCD2; and 493 (laplace) and 203 (rbf) for RAD54L - FANCD2; RAD-1/18/50/51/51C/54B/54L were found to be down regulated w.r.t FANCD2OS. These are reflected in rankings of 693 (laplace) and 1146450 (rbf) for RAD1 - FANCD2OS; 1472 (laplace), 526 (linear) and 239 (rbf) for RAD18 - FANCD2OS; 178 (laplace) and 1534 (linear) for RAD50 - FANCD2OS; 1080 (linear) and 1226 (rbf) for RAD51 - FANCD2OS; 1297 (laplace), 977 (linear) and 1237 (rbf) for RAD51C - FANCD2OS; 475 (laplace), 1367 (linear) for RAD54B - FANCD2OS; 1227 (linear) and 252 (rbf) for RAD54L - FANCD2OS; RAD-1/18/50/51/51AP1/51C/54B/54L455 were found to be down regulated w.r.t FANCF. These are reflected in rankings of 25 [23] J. Garc´ ıa-Luis, F. Mach´ ın, Fanconi anaemia-like mph1 helicase backs up rad54 and rad5 to circumvent replication stress-driven chromosome bridges, Genes 9 (2018) 558. [24] B. Madan, Z. Ke, N. Harmston, S. Y. Ho, A. Frois, J. Alam, D. A. Jeyaraj, V. Pendharkar, K. Ghosh, I. H. Virshup,590 et al., Wnt addiction of genetically defined cancers reversed by porcn inhibition, Oncogene 35 (2016) 2197. 32