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 Rv2478c/-

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

	Rv1528c/papA4	Rv2478c/-
Fe_supp_jason_reseq	-1.628	0.129
low_pH_jason_reseq	-0.105	0.599
NO_jason_reseq	-0.73	0.483
B6_jason_reseq	0.215	1.074
MHCII_jason_reseq	1.047	1.038
Isoniazid02	0.511	0.458
Rifampicin4	-0.341	0.395
Ethambutol3	0.743	0.567
Meropenem3	0.67	0.334
Vancomycin16	0.308	0.669
Rv2680_day32	-1.157	-0.119
H37Rv_KO_MarP	-0.332	0.412
hypoxia_3wks	-0.064	0.602
hypoxia_6wks	-0.441	0.257
glycerol	0.366	0.355
cholesterol	-0.374	0.827
AJ	0.526	-0.146
Bibs02	1.032	0.109
Bibs02c	0.038	1.082
BL6	-0.945	0.062
BL6a	0.489	0.517
BXD01	-0.135	0.0
BXD010	-1.142	0.173
BXD011	0.387	-0.855
BXD03	0.058	0.504
BXD04	0.733	-0.295
BXD05	-0.206	0.453
BXD06	0.214	0.071
BXD07	-0.436	-0.077
BXD08	0.119	0.019
BXD09	0.164	-0.025
CAST	0.953	0.813
CCcont	-0.772	-0.208
DS01	0.695	0.63
DS02	-0.317	-0.758
DS04	1.476	1.19
DS0c	1.07	0.776
GP01	-2.152	-2.067
GP02	-1.947	-0.872
GP0c	-2.492	-1.695
NOD	0.937	0.636
NZO	0.587	0.863
PWK	0.685	0.917
H37Rv_KO_CtpC	-0.191	-1.243
H37Rv_KO_CtpD	0.853	0.842
H37Rv_KO_Rv1272	0.89	-0.395
H37Rv_KO_SugABC	0.401	-0.659
H37Rv_KO_MbtN	0.925	1.059
Trans05	-0.347	-0.22
macrophage_unactivated	-0.732	0.23
IL1	-0.409	-0.246
Rapamycin	-0.396	-0.562
Tcell	-0.055	0.417
GMCSF	0.108	1.296
IFNab	0.193	-0.115
IFNg	-0.158	-0.313
IFNg_GMCSF1	0.079	0.584
Rv1432_day32	0.0	0.389
Rv1565c_day32	0.602	0.851
secA2_input	0.643	0.185
delta_Rv3594	-0.249	0.821
delta_Rv3717	-1.073	0.143
delta_Rv3811	-0.968	0.317
delta_Rv0954	-0.261	0.173
PonA1	-0.452	-0.563
EccD1_KO	-0.605	-0.204
EspI_KO	-0.724	-0.445
PE35_KO	0.149	-0.298
PPE68_KO	-0.528	-0.054
glycerol2	-0.01	0.164
lignocerate	-0.163	0.089
oleate	0.276	0.544
phosphatidylcholine	0.083	0.392
acetate	-0.286	-0.444
glucAc	-0.602	-0.468
Rv0950ko	0.51	-0.88
Rv1096ko	-0.359	-1.218
Rv3684ko	-0.72	-0.884
delta_otsA_trehalose	-0.145	-0.164