Analyze GSE89540 with reference data using SCAN (gene sets)

Investigate the expression of key genes potentially involed in DBA pathogenesis

Read in processed data and a subset of gene sets.

Perform differential expression analysis for SCAN normalized gene sets

Perform differential expression analysis for RMA normalized gene sets

Check for differential expression of key genes.

combined.RMA.GSE41817.table["ALAS2",]

##            logFC  AveExpr          t   P.Value adj.P.Val         B
## ALAS2 -0.5505513 9.661347 -0.4643075 0.6528458 0.9838692 -5.490981

combined.RMA.GSE41817.table["GATA1",]

##            logFC  AveExpr         t   P.Value adj.P.Val         B
## GATA1 -0.1546032 7.470615 -0.724291 0.4862765 0.9769421 -5.349734

combined.RMA.GSE41817.table["HBB",]

##          logFC  AveExpr         t   P.Value adj.P.Val         B
## HBB 0.03214361 14.54898 0.1516793 0.8826006 0.9924939 -5.581608

combined.RMA.GSE89540.table.DBAvControl["ALAS2",]

##           logFC  AveExpr        t   P.Value adj.P.Val         B
## ALAS2 0.8265718 10.14716 1.691234 0.1047621 0.4713699 -4.347265

combined.RMA.GSE89540.table.DBAvControl["GATA1",]

##           logFC  AveExpr        t   P.Value adj.P.Val         B
## GATA1 0.2458813 9.988942 1.417341 0.1702439  0.530045 -4.679587

combined.RMA.GSE89540.table.DBAvControl["HBB",]

##         logFC  AveExpr        t   P.Value adj.P.Val         B
## HBB 0.2207331 7.126908 1.310875 0.2032776 0.5632296 -4.796093

combined.RMA.GSE89540.table.DBAvControl["ALAS2",]

##           logFC  AveExpr        t   P.Value adj.P.Val         B
## ALAS2 0.8265718 10.14716 1.691234 0.1047621 0.4713699 -4.347265

combined.RMA.GSE89540.table.DBAvControl["GATA1",]

##           logFC  AveExpr        t   P.Value adj.P.Val         B
## GATA1 0.2458813 9.988942 1.417341 0.1702439  0.530045 -4.679587

combined.RMA.GSE89540.table.DBAvControl["HBB",]

##         logFC  AveExpr        t   P.Value adj.P.Val         B
## HBB 0.2207331 7.126908 1.310875 0.2032776 0.5632296 -4.796093

combined.RMA.GSE89540.table.DBA_GATA1vControl["ALAS2",]

##            logFC  AveExpr          t   P.Value adj.P.Val         B
## ALAS2 -0.4852665 10.14716 -0.6814724 0.5026091 0.9997145 -4.910827

combined.RMA.GSE89540.table.DBA_GATA1vControl["GATA1",]

##           logFC  AveExpr         t   P.Value adj.P.Val        B
## GATA1 0.2441328 9.988942 0.9658723 0.3444962 0.9997145 -4.76994

combined.RMA.GSE89540.table.DBA_GATA1vControl["HBB",]

##          logFC  AveExpr         t   P.Value adj.P.Val         B
## HBB -0.3027845 7.126908 -1.234162 0.2300276 0.9997145 -4.598055

combined.RMA.GSE89540.table.DBA_GATA1vDBA["ALAS2",]

##           logFC  AveExpr         t    P.Value adj.P.Val         B
## ALAS2 -1.311838 10.14716 -1.914837 0.06846548  0.841491 -3.983151

combined.RMA.GSE89540.table.DBA_GATA1vDBA["GATA1",]

##              logFC  AveExpr            t   P.Value adj.P.Val         B
## GATA1 -0.001748427 9.988942 -0.007189932 0.9943274 0.9987077 -5.269669

combined.RMA.GSE89540.table.DBA_GATA1vDBA["HBB",]

##          logFC  AveExpr         t   P.Value adj.P.Val         B
## HBB -0.5235176 7.126908 -2.217959 0.0370743  0.841491 -3.596159

combined.SCAN.GSE41817.table["ALAS2",]

##             logFC  AveExpr          t   P.Value adj.P.Val         B
## ALAS2 -0.09132189 1.419722 -0.1640895 0.8732244 0.9819691 -5.718714

combined.SCAN.GSE41817.table["GATA1",]

##             logFC   AveExpr          t   P.Value adj.P.Val         B
## GATA1 -0.02416415 0.2051725 -0.3425272 0.7396831 0.9600617 -5.674126

combined.SCAN.GSE41817.table["HBB",]

##           logFC  AveExpr          t   P.Value adj.P.Val         B
## HBB -0.08926071 3.521007 -0.6092507 0.5571654 0.9300153 -5.551434

combined.SCAN.GSE89540.table.DBAvControl["ALAS2",]

##           logFC AveExpr        t    P.Value adj.P.Val         B
## ALAS2 0.5103011 2.28445 1.722819 0.09971455 0.4576909 -4.341236

combined.SCAN.GSE89540.table.DBAvControl["GATA1",]

##           logFC  AveExpr        t   P.Value adj.P.Val         B
## GATA1 0.1523924 2.112046 1.343062 0.1936826 0.5514939 -4.805164

combined.SCAN.GSE89540.table.DBAvControl["HBB",]

##         logFC  AveExpr        t    P.Value adj.P.Val         B
## HBB 0.2195968 1.375869 1.906629 0.07043691 0.4360524 -4.087057

combined.SCAN.GSE89540.table.DBAvControl["ALAS2",]

##           logFC AveExpr        t    P.Value adj.P.Val         B
## ALAS2 0.5103011 2.28445 1.722819 0.09971455 0.4576909 -4.341236

combined.SCAN.GSE89540.table.DBAvControl["GATA1",]

##           logFC  AveExpr        t   P.Value adj.P.Val         B
## GATA1 0.1523924 2.112046 1.343062 0.1936826 0.5514939 -4.805164

combined.SCAN.GSE89540.table.DBAvControl["HBB",]

##         logFC  AveExpr        t    P.Value adj.P.Val         B
## HBB 0.2195968 1.375869 1.906629 0.07043691 0.4360524 -4.087057

combined.SCAN.GSE89540.table.DBA_GATA1vControl["ALAS2",]

##            logFC AveExpr          t  P.Value adj.P.Val         B
## ALAS2 -0.2618262 2.28445 -0.6066959 0.550599 0.9998879 -5.108358

combined.SCAN.GSE89540.table.DBA_GATA1vControl["GATA1",]

##              logFC  AveExpr           t   P.Value adj.P.Val         B
## GATA1 -0.008369694 2.112046 -0.05062757 0.9601039 0.9998879 -5.246356

combined.SCAN.GSE89540.table.DBA_GATA1vControl["HBB",]

##           logFC  AveExpr          t   P.Value adj.P.Val         B
## HBB -0.08145771 1.375869 -0.4854194 0.6324379 0.9998879 -5.158011

combined.SCAN.GSE89540.table.DBA_GATA1vDBA["ALAS2",]

##            logFC AveExpr         t    P.Value adj.P.Val         B
## ALAS2 -0.7721273 2.28445 -1.859647 0.07709698  0.982447 -4.054036

combined.SCAN.GSE89540.table.DBA_GATA1vDBA["GATA1",]

##            logFC  AveExpr         t   P.Value adj.P.Val         B
## GATA1 -0.1607621 2.112046 -1.010752 0.3237156  0.982447 -4.889537

combined.SCAN.GSE89540.table.DBA_GATA1vDBA["HBB",]

##          logFC  AveExpr        t   P.Value adj.P.Val         B
## HBB -0.3010545 1.375869 -1.86472 0.0763522  0.982447 -4.047981

Create synthetic normal and normalize O’Brien et al. expression set

Check for differential expression of key genes in synthetic normal and after removing synthetic normal from O’Brien et al. expression set

#Synthetic normal
combined.RMA.GSE89540.sn.table.DBAvControl["ALAS2",]

##          logFC  AveExpr        t     P.Value  adj.P.Val         B
## ALAS2 1.417284 10.24341 2.902705 0.008663004 0.05770758 -2.476174

combined.RMA.GSE89540.sn.table.DBAvControl["GATA1",]

##            logFC  AveExpr         t    P.Value adj.P.Val         B
## GATA1 -0.1123234 9.166166 -2.393998 0.02634278 0.0836422 -3.384987

combined.RMA.GSE89540.sn.table.DBAvControl["HBB",]

##          logFC  AveExpr        t   P.Value adj.P.Val         B
## HBB 0.03936273 14.40339 1.175115 0.2534412 0.3840489 -5.100835

combined.RMA.GSE89540.sn.table.DBAvControl["ALAS2",]

##          logFC  AveExpr        t     P.Value  adj.P.Val         B
## ALAS2 1.417284 10.24341 2.902705 0.008663004 0.05770758 -2.476174

combined.RMA.GSE89540.sn.table.DBAvControl["GATA1",]

##            logFC  AveExpr         t    P.Value adj.P.Val         B
## GATA1 -0.1123234 9.166166 -2.393998 0.02634278 0.0836422 -3.384987

combined.RMA.GSE89540.sn.table.DBAvControl["HBB",]

##          logFC  AveExpr        t   P.Value adj.P.Val         B
## HBB 0.03936273 14.40339 1.175115 0.2534412 0.3840489 -5.100835

combined.RMA.GSE89540.sn.table.DBA_GATA1vControl["ALAS2",]

##           logFC  AveExpr        t   P.Value adj.P.Val         B
## ALAS2 0.1806823 10.24341 0.253984 0.8020424 0.8901072 -5.378335

combined.RMA.GSE89540.sn.table.DBA_GATA1vControl["GATA1",]

##            logFC  AveExpr         t  P.Value adj.P.Val         B
## GATA1 -0.1500157 9.166166 -2.194497 0.039895 0.5575744 -3.625563

combined.RMA.GSE89540.sn.table.DBA_GATA1vControl["HBB",]

##            logFC  AveExpr          t   P.Value adj.P.Val         B
## HBB -0.007314466 14.40339 -0.1498727 0.8823324 0.9374309 -5.395979

combined.RMA.GSE89540.sn.table.DBA_GATA1vDBA["ALAS2",]

##           logFC  AveExpr         t    P.Value adj.P.Val         B
## ALAS2 -1.236602 10.24341 -1.806776 0.08552529 0.3635934 -4.161713

combined.RMA.GSE89540.sn.table.DBA_GATA1vDBA["GATA1",]

##            logFC  AveExpr          t   P.Value adj.P.Val         B
## GATA1 -0.0376923 9.166166 -0.5731056 0.5728177 0.7711283 -5.297733

combined.RMA.GSE89540.sn.table.DBA_GATA1vDBA["HBB",]

##          logFC  AveExpr          t   P.Value adj.P.Val         B
## HBB -0.0466772 14.40339 -0.9940962 0.3317862  0.591083 -5.026388

#Normalized
combined.RMA.GSE89540.sn.norm.table.DBAvControl["ALAS2",]

##             logFC   AveExpr           t   P.Value adj.P.Val         B
## ALAS2 -0.02958282 -0.661185 -0.03202959 0.9747308 0.9900751 -5.670345

combined.RMA.GSE89540.sn.norm.table.DBAvControl["GATA1",]

##           logFC    AveExpr        t    P.Value adj.P.Val         B
## GATA1 0.5544215 -0.6197297 1.877433 0.07348117 0.4295649 -4.172982

combined.RMA.GSE89540.sn.norm.table.DBAvControl["HBB",]

##         logFC   AveExpr        t   P.Value adj.P.Val         B
## HBB 0.2711627 -3.961081 1.122357 0.2735427 0.6373178 -5.107011

combined.RMA.GSE89540.sn.norm.table.DBAvControl["ALAS2",]

##             logFC   AveExpr           t   P.Value adj.P.Val         B
## ALAS2 -0.02958282 -0.661185 -0.03202959 0.9747308 0.9900751 -5.670345

combined.RMA.GSE89540.sn.norm.table.DBAvControl["GATA1",]

##           logFC    AveExpr        t    P.Value adj.P.Val         B
## GATA1 0.5544215 -0.6197297 1.877433 0.07348117 0.4295649 -4.172982

combined.RMA.GSE89540.sn.norm.table.DBAvControl["HBB",]

##         logFC   AveExpr        t   P.Value adj.P.Val         B
## HBB 0.2711627 -3.961081 1.122357 0.2735427 0.6373178 -5.107011

combined.RMA.GSE89540.sn.norm.table.DBA_GATA1vControl["ALAS2",]

##            logFC   AveExpr          t   P.Value adj.P.Val         B
## ALAS2 -0.9953784 -0.661185 -0.7396815 0.4671397 0.9997934 -4.663227

combined.RMA.GSE89540.sn.norm.table.DBA_GATA1vControl["GATA1",]

##           logFC    AveExpr       t  P.Value adj.P.Val         B
## GATA1 0.5889701 -0.6197297 1.36887 0.184549 0.9997934 -4.514909

combined.RMA.GSE89540.sn.norm.table.DBA_GATA1vControl["HBB",]

##          logFC   AveExpr         t   P.Value adj.P.Val         B
## HBB -0.4186402 -3.961081 -1.189288 0.2467237 0.9997934 -4.564614

combined.RMA.GSE89540.sn.norm.table.DBA_GATA1vDBA["ALAS2",]

##            logFC   AveExpr          t   P.Value adj.P.Val         B
## ALAS2 -0.9657956 -0.661185 -0.7459769 0.4634028 0.9335219 -4.993166

combined.RMA.GSE89540.sn.norm.table.DBA_GATA1vDBA["GATA1",]

##           logFC    AveExpr          t  P.Value adj.P.Val         B
## GATA1 0.0345486 -0.6197297 0.08346093 0.934223 0.9924475 -5.190056

combined.RMA.GSE89540.sn.norm.table.DBA_GATA1vDBA["HBB",]

##         logFC   AveExpr         t   P.Value adj.P.Val         B
## HBB -0.689803 -3.961081 -2.036829 0.0535984 0.8306519 -3.842394