GRNmap Testing and Results

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Presentation transcript:

GRNmap Testing and Results Natalie Williams Brandon Klein October 31, 2016

Last week, we tested GRNmap with our 5 database-generated Networks. 1) Input sheets were made for five database-derived networks (wt, dCIN5, dGLN3, dHAP4, dZAP1). 2) Model runs were performed for each network. 3) Preliminary results from the runs are presented here. 4) We will work towards developing an in depth analysis of these results in the coming weeks.

Unweighted visualization of the 5 database-generated GRNs via GRNSight dGLN3 Unweighted Network WT Unweighted Network dCIN5 Unweighted Network dZAP1 Unweighted Network dHAP4 Unweighted Network

Weighted GRNSight visualizations of the database-derived GRNs from all 5 strains WT Weighted Network dCIN5 Weighted Network dGLN3 Weighted Network dHAP4 Weighted Network dZAP1 Weighted Network

WT GRNmap Testing Results As of: 2016 Oct. 30 WT Information: 16 Nodes (Genes) 36 Edges Network composed of the following genes: ABF1 ACE2 AFT2 ASF1 ASH1 CIN5 GCN4 GLN3 HAP4 HMO1 MSN2 SFP1 SWI4 YHP1 YOX1 ZAP1

Parameter Outputs - WT Parameter Value Penalty Term 2.5923 LSE 0.8194 minLSE 0.5768 LSE:minLSE ratio 1.4206 Iteration Count 109718

GRNmap Output Estimation of ABF1, ACE2, AFT2, AND ASF1

GRNmap Output Estimation of ASH1, CIN5, GCN4, AND GLN3

GRNmap Output Estimation of HAP4, HMO1, MSN2, AND SFP1

GRNmap Output Estimation of SWI4, YHP1, YOX1, AND ZAP1

Weighted WT Network appears to have more activation than repression of genes within the network.

Optimized Production Rates and Threshold B Values for wt Network id production_rate threshold_b ABF1 0.057591382 0.057591 ACE2 0.133860771 0.262124 AFT2 0.290004958 4.516856 ASF1 0.158179715 1.358124 ASH1 1.529886194 0.764114 CIN5 1.152815988 2.697564 GCN4 0.181216029 2.422825 GLN3 0.360109759 1.344126 HAP4 2.344771437 -1.74514 HMO1 0.483290667 1.312883 MSN2 0.573852542 0.89613 SFP1 1.006631277 1.243381 SWI4 0.227818344 -3.39406 YHP1 0.151302376 0.312824 YOX1 0.785593453 2.981617 ZAP1 0.12653347 0.126533

dCIN5 GRNmap Testing Results As of: 2016 Oct. 26 dCIN5 Information: 15 Nodes (Genes) 20 Edges Network Composed of the following genes: ACE2 CIN5 GCR2 GLN3 HAP4 MGA2 MSN2 PDR1 RDS3 SFP1 STB5 SWI5 YHP1 YOX1 ZAP1

Parameter Outputs – dCIN5 Value Penalty Term 1.9396 LSE 0.7200 minLSE 0.4883 LSE:minLSE 1.4745 Iteration count 32595

GRNmap Output Estimation of ACE2, CIN5, GCR2 AND GLN3

GRNmap Output Estimation of HAP4, MGA2, MSN2, AND PDR1

GRNmap Output Estimation of RDS3, SFP1, STB5, AND SWI5

GRNmap Output Estimation of YHP1, YOX1 AND ZAP1

Weighted dCIN5 Network from GRNSight appears to have an equal distribution of high activation and repression.

Optimized Production Rates and Threshold B Values for dCIN5 Network id production_rate threshold_b ACE2 0.239035969 1.140363 CIN5 1.937039256 -1.59358 GCR2 0.238368923 0.238369 GLN3 0.333099398 0.373651 HAP4 1.021627291 3.900532 MGA2 0.271687006 -0.02688 MSN2 2.507572912 -1.78041 PDR1 0.717322746 -0.42142 RDS3 0.220922587 0.567369 SFP1 1.169085767 2.315616 STB5 0.321901481 0.857352 SWI5 1.386398987 -1.10279 YHP1 0.858036572 -1.26956 YOX1 1.494446257 -0.97951 ZAP1 0.142220917 0.142221

dGLN3 GRNmap Testing Results As of: 2016 Oct. 30 dGLN3 Information: 14 Nodes (Genes) 35 Edges Network composed of the following genes: CIN5 CYC8 GCR2 GLN3 HAP4 HMO1 MSN2 MSN4 SFP1 SWI4 SWI5 TEC1 YHP1 YOX1

Parameter Outputs – dGLN3 Value LSE 0.6994 Penalty 1.7895 min LSE 0.5379 Iteration count 78,124 LSE/minLSE ratio 1.300

GRNmap Output Estimation of CIN5, CYC8, GCR2, and GLN3

GRNmap Output Estimation of HAP4, HMO1, MSN2, and MSN4

GRNmap Output Estimation of SFP1, SWI4, and SWI5

GRNmap Output Estimation of TEC1, YHP1, and YOX1

Unweighted dGLN3 Network

Weighted dGLN3 Network

Optimized Production Rates and Threshold B Values for the dGLN3 Network id production_rate threshold_b CIN5 1.271003641 0.209399466 CYC8 0.160845844 0.950363449 GCR2 0.220370375 GLN3 0.28447758 1.482407766 HAP4 1.256925872 0.614245955 HMO1 0.182926186 0.870922377 MSN2 0.520156519 1.661419406 MSN4 1.320347752 -0.013479776 SFP1 1.19732936 -0.021415072 SWI4 0.287798399 0.76607819 SWI5 2.305777244 -2.553877634 TEC1 1.576533679 0.351001393 YHP1 0.53884153 1.108341513 YOX1 0.792511916 1.692328334

dHAP4 GRNmap Testing Results As of: 2016 Oct. 30 dHAP4 Information: 15 Nodes (Genes) 28 Edges Network composed of the following genes: ACE2 ASH1 CIN5 GCR2 GLN3 HAP4 HMO1 MSN2 SFP1 STB5 SWI4 SWI5 YHP1 YOX1 ZAP1

Parameter Outputs – dhap4 Value LSE 0.6919 Penalty 2.3443 min LSE 0.4851 iteration count 62139 LSE/minLSE ratio 1.4263

GRNmap Output Estimation of ACE2, ASH1, CIN5, and GCR2

GRNmap Output Estimation of GLN3, HAP4, HMO1, and MSN2

GRNmap Output Estimation of SFP1, STB5, SWI4, and SWI5

GRNmap Output Estimation of YHP1, YOX1, and ZAP1

Unweighted dHAP4 Network

Weighted dHAP4 Network

Optimized Production Rates and Threshold B Values for the dHAP4 Network id production_rate threshold_b ACE2 0.163234325 0.600247905 ASH1 2.026770243 -1.788383776 CIN5 0.951135552 2.368983232 GCR2 0.235110128 GLN3 0.287841401 0.820555924 HAP4 1.672581844 0.726615646 HMO1 0.23866431 0.968024053 MSN2 0.882424058 4.748924118 SFP1 1.209396426 1.039919814 STB5 0.320388323 0.57712108 SWI4 0.241176223 0.326154591 SWI5 1.249745969 -0.591006185 YHP1 0.341078303 2.30425228 YOX1 0.864626626 2.095374344 ZAP1 0.129813716

dZAP1 GRNmap Testing Results As of: 2016 Oct. 30 dZAP1 Information: 16 Nodes (Genes) 27 Edges Network composed of the following genes: ABF1 ACE2 CIN5 CST6 GCN4 GCR2 GLN3 HAP4 HMO1 HSF1 MCM1 MGA2 MSN2 MSN4 SWI4 ZAP1

Parameter Outputs – dZAP1 Value LSE 0.8602 Penalty 1.8276 min LSE 0.6156 iteration count 76769 LSE/minLSE ratio 1.3973

GRNmap Output Estimation of ABF1, ACE2, CIN5, and CST6

GRNmap Output Estimation of GCN4, GCR2, GLN3, AND HAP4

GRNmap Output Estimation of HMO1, HSF1, MCM1, and MGA2

GRNmap Output Estimation of MSN2, MSN4, SWI4, AND ZAP1

Unweighted dZAP1 Network

Weighted dZAP1 Network

Optimized Production Rates and Threshold B Values for the dZAP1 Network id production_rate threshold_b ABF1 0.05756589 ACE2 0.231454349 1.538999218 CIN5 1.915680925 -0.536934415 CST6 0.291666931 -0.023546341 GCN4 0.045606823 -0.942389874 GCR2 0.227795509 GLN3 1.357203575 -0.447653587 HAP4 1.704620101 0.170199964 HMO1 0.238992333 0.384936848 HSF1 0.107908965 0.095031078 MCM1 0.142935955 0.264279283 MGA2 0.307594235 -0.039708706 MSN2 1.353883241 -0.64778282 MSN4 1.405376368 1.717458691 SWI4 0.21276404 -2.744608001 ZAP1 0.130661697