Agilent GeneSpring Mass Profiler Professional X Y X Y 2 Chen, P; Popovich, P. Correlation:Parametric and Nonparametric Measures Sage Publications, 200
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1 Agilent GeneSpring Mass Profiler Professional X Y X Y 2 Chen, P; Popovich, P. Correlation:Parametric and Nonparametric Measures Sage Publications, 2002 Pritha Aggarwal, Durairaj Renu, and Pramila Tata Strand Life Sciences Bangalore, India Michael Rosenberg Agilent Technologies, Inc. (NGS) GeneSpring/Mass Profiler Professional (MPP) GeneSpring/MPP 13.0 Santa Clara, California, USA
2 1 2 ( X Y X Y ( org/wiki/pearson_product-moment_correlation_ coefficient) ( ) GeneSpring/MPP mirna mrna 2 ( 1 R 2 R) Experiment 1. X Y (CC) Experiment X Y 2
3 GeneSpring/MPP (Experiment) Workflow Browser Experiment 2 Experiment Experiment 2 Experiment (MOA) Experiment GeneSpring 1 GeneSpring Experiment Experiment 2 Experiment 2 3 Experiment MOA Experiment : GeneSpring/MPP Experiment 1 MOA Experiment 2 Experiment 2 1. GeneSpring Experiment 2 Experiment mrna mirna RTPCR DNA-Seq RNA-Seq * smallrna-seq * * RNA-Seq smallrna-seq Experiment Strand NGS v2.1 ( GeneSpring : GeneSpring Experiment : GeneSpring 13.0 GeneSpring ( ) (Correlation coefficient) (Correlation heatmap) CC mr1 mr2 mr3 mr4 mr5 mr6 mr7 mr8 mr9 mr10 mr11 mr12 mr13 mr14 mr15 mr16 mr17 mr18 mr19 mr20 mr21 mr22 mr23 mr24 mr25 mr1 mr2 mr3 mr4 mr5 mr6 mr7 mr8 mr9 mr10 mr11 mr12 mr13 mr14 mr15 mr16 mr17 mr18 mr19 mr20 mr21 mr22 mr23 mr24 mr25 Correlation value by color Experiment ( ) () 3
4 ( ) (Correlation coefficients) (Correlation heatmap) CC hsa-mir-142-3p 3 Correlation value by color hsa-mir Experiment Experiment Experiment 1 Experiment 2 2 Experiment 2 m Experiment 1 n Experiment 2 m+n X Y X Y Experiment MOA Experiment 2 Experiment ( +1) Experiment MOA Experiment 2 3 ( ) MOA 4 Experiment Experiment ( 5) A Toggle ON B Toggle OFF hsa-mir-142-3p 3 hsa-mir hsa-mir MOA ON/OFF (A) (B) Experiment 4
5 GeneSpring/MPP (Fold change) p Fold change p / ( 6A) ( AND) P4HA2 COL1A1 THBS1 CAST SHC1 TGOLN2 ANXA2 TGFBI SLC10A3 DSE P4HA2 COL1A1 THBS1 CAST SHC1 TGOLN2 ANXA2 TGFBI SLC10A3 DSE Excel GeneSpring 6A ( 6B) ( 6 (RTK)) 5. Experiment 1 Experiment 6 RTK RTK MOA Experiment 1 2 A Numerical filter Categorical filter Text query filter Heatmap was filtered to show only members of the RTK pathway; the pathway information was imported from an external file BRAF CBL EGFR ERBB2 ERBB3 FGFR1 FGFR2 GRB2 MET NF1 NRAS PDGFRA PDGFRB RAF1 SPRY2 BRAF CBL EGFR ERBB2 ERBB3 FGFR1 FGFR2 GRB2 MET NF1 NRAS PDGFRA PDGFRB RAF1 SPRY2 B External file format Identifier Pathway AKT1 AKT AKT2 AKT AKT3 AKT ARAF RKT ATM P53 BRAF RKT CBL P53 CCND1 P53 CCND2 RKT CCNE1 RB CDKN2A RB CDKN2B RB CDKN2C RB E2F1 RB EGFR RKT EP300 P53 ERBB2 RKT 6. A) Fold Change (FC) Pathway Genes_GBM 30 ( Categorical filter ) 30 ( Text Query filter ) B) 5
6 GeneSpring/MPP 2 Experiment MOA Experiment Experiment ( 7) MOA Experiment 2. GeneSpring ( ) Euclidean Squared Euclidean Manhattan (Cityblock) Maximum (Chebychev) Minimum Differential Canberra Harmonic Pearson s Centered Pearson s Uncentered (Cosine) Pearson s Centered Absolute Pearson s Uncentered Absolute Average Centroid Ward s Median Single Complete exp1/exp1 CCs exp2/exp1 CCs exp1/exp2 CCs exp2/exp2 CCs hsa-mir-142-3p 3 hsa-mir-142-3p 3 7. MOA Experiment 6
7 ( 8) GeneSpring/MPP 0 ( 9) GeneSpring 8. Highlighted entity Unmatched entity correlation displayed in background color Selected entity hsa-mir-142-3p 3 hsa-mir-142-3p
8 GeneSpring/ MPP Experiment Experiment ( 1) Experiment MOA Experiment 3 Gene Experiment ( 10) Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene (Plasmodium falciparum) ph ph 9.0 ph 2.0 ph 7.0 Tube no. NRBC IRBC at 10 % SLO 250 stock units Set A Set B Set C µl ph 2 ph 7 ph µl ph 2 ph 7 ph µl ph 2 ph 7 ph µl ph 2 ph 7 ph µl 10 µl ph 2 ph 7 ph µl 10 µl ph 2 ph 7 ph µl 10 µl ph 2 ph 7 ph µl 10 µl ph 2 ph 7 ph µl ph 2 ph 7 ph µl ph 2 ph 7 ph µl ph 2 ph 7 ph µl ph 2 ph 7 ph µl 10 µl ph 2 ph 7 ph µl 10 µl ph 2 ph 7 ph µl 10 µl ph 2 ph 7 ph µl 10 µl ph 2 ph 7 ph (NRBC = RBC IRBC = RBC) ph 8
9 1. T C G A Research Network ( gov/) 2. Sana, T. R Global Mass Spectrometry Based Metabolomics Profiling of Erythrocytes Infected with Plasmodium falciparum.plos ONE 2013, 8(4): e doi: /journal. pone
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12 ( ) Mass Profiler Professional G3835AA Mass Profiler Professional (MPP) Perpetual G9274AA Mass Profiler Professional (MPP) Perpetual G3836AA MPP Perpetual G9275AA MPP Perpetual G9277AA (Perpetual) Agilent MSD ChemStation MassHunter MPP G9281AA Mass Profiler Pro (MPP) Concurrent 1 1 G9282AA Mass Profiler Pro (MPP) Concurrent G9281AA GeneSpring G5886AA GeneSpring GX Standard Perpetual Academic + 1 SMA G5887AA GeneSpring GX Standard Perpetual Commercial + 1 SMA G5888AA GeneSpring GX Standard - Academic G5889AA GeneSpring GX Standard - Commercial G5890AA GeneSpring GX Concurrent Perpetual Academic + 1 SMA G5891AA GeneSpring GX Concurrent Perpetual Commercial + 1 SMA G5892AA GeneSpring GX Concurrent Perpetual - Academic G5893AA GeneSpring GX Concurrent Perpetual - Commercial G3784AA GeneSpring GX 1 - Academic G3782AA GeneSpring GX 2 - Academic G3780AA GeneSpring GX 3 - Academic G3783AA GeneSpring GX Concurrent 1 - Academic G3781AA GeneSpring GX Concurrent 2 - Academic G3779AA GeneSpring GX Concurrent 3 - Academic G3778AA GeneSpring GX 1 - Commercial G3776AA GeneSpring GX 2 - Commercial G3774AA GeneSpring GX 3 - Commercial G3777AA GeneSpring GXConcurrent 1 - Commercial G3775AA GeneSpring GXConcurrent 2 - Commercial G3773AA GeneSpring GXConcurrent 3 - Commercial Agilent Technologies, Inc., 2014 Published in Japan, September 29, JAJP
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