TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1528c/papA4:

update plot	correlation	link to info on gene
Rv2478c/-	(cc=0.555)	info on Rv2478c/-
Rv1516c/-	(cc=0.5471)	info on Rv1516c/-
Rv0828c/-	(cc=0.4906)	info on Rv0828c/-
Rv1542c/glbN	(cc=0.4853)	info on Rv1542c/glbN
Rv0388c/PPE9	(cc=0.4808)	info on Rv0388c/PPE9
Rv1453/-	(cc=0.4547)	info on Rv1453/-
Rv2331/-	(cc=0.442)	info on Rv2331/-
Rv3103c/-	(cc=0.4399)	info on Rv3103c/-
Rv3368c/-	(cc=0.436)	info on Rv3368c/-
Rv0141c/-	(cc=0.4268)	info on Rv0141c/-

Correlation of Rv1528c/papA4 with Rv2331/-

Normalized LFCs for Rv1528c/papA4:
(description and provenance of datasets)

	Rv1528c/papA4	Rv2331/-
Fe_supp_jason_reseq	-1.628	0.069
low_pH_jason_reseq	-0.105	-0.589
NO_jason_reseq	-0.73	0.961
B6_jason_reseq	0.215	1.602
MHCII_jason_reseq	1.047	0.799
Isoniazid02	0.511	0.511
Rifampicin4	-0.341	-1.338
Ethambutol3	0.743	-0.336
Meropenem3	0.67	-0.456
Vancomycin16	0.308	-0.348
Rv2680_day32	-1.157	-2.26
H37Rv_KO_MarP	-0.332	-0.056
hypoxia_3wks	-0.064	0.415
hypoxia_6wks	-0.441	0.357
glycerol	0.366	-1.695
cholesterol	-0.374	-0.126
AJ	0.526	0.486
Bibs02	1.032	0.611
Bibs02c	0.038	0.259
BL6	-0.945	1.479
BL6a	0.489	0.343
BXD01	-0.135	0.273
BXD010	-1.142	0.322
BXD011	0.387	0.333
BXD03	0.058	0.273
BXD04	0.733	1.132
BXD05	-0.206	0.766
BXD06	0.214	0.774
BXD07	-0.436	0.66
BXD08	0.119	0.353
BXD09	0.164	0.443
CAST	0.953	0.739
CCcont	-0.772	-0.587
DS01	0.695	0.0
DS02	-0.317	0.057
DS04	1.476	0.586
DS0c	1.07	0.251
GP01	-2.152	-3.176
GP02	-1.947	-1.929
GP0c	-2.492	-3.762
NOD	0.937	1.593
NZO	0.587	-0.27
PWK	0.685	0.043
H37Rv_KO_CtpC	-0.191	-1.923
H37Rv_KO_CtpD	0.853	0.579
H37Rv_KO_Rv1272	0.89	0.946
H37Rv_KO_SugABC	0.401	-0.053
H37Rv_KO_MbtN	0.925	-2.132
Trans05	-0.347	0.629
macrophage_unactivated	-0.732	-1.326
IL1	-0.409	0.742
Rapamycin	-0.396	-0.175
Tcell	-0.055	0.502
GMCSF	0.108	-0.422
IFNab	0.193	-1.956
IFNg	-0.158	-0.521
IFNg_GMCSF1	0.079	-0.666
Rv1432_day32	0.0	0.314
Rv1565c_day32	0.602	-0.245
secA2_input	0.643	0.618
delta_Rv3594	-0.249	0.477
delta_Rv3717	-1.073	-0.458
delta_Rv3811	-0.968	0.269
delta_Rv0954	-0.261	0.249
PonA1	-0.452	0.407
EccD1_KO	-0.605	0.599
EspI_KO	-0.724	0.519
PE35_KO	0.149	0.318
PPE68_KO	-0.528	0.202
glycerol2	-0.01	0.207
lignocerate	-0.163	0.81
oleate	0.276	-0.362
phosphatidylcholine	0.083	0.861
acetate	-0.286	-0.18
glucAc	-0.602	0.439
Rv0950ko	0.51	-0.443
Rv1096ko	-0.359	-0.98
Rv3684ko	-0.72	-1.461
delta_otsA_trehalose	-0.145	-0.364