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 Rv0114/gmhB:

update plot	correlation	link to info on gene
Rv3429/PPE59	(cc=0.5625)	info on Rv3429/PPE59
Rv1593c/-	(cc=0.5324)	info on Rv1593c/-
Rv1500/-	(cc=0.5287)	info on Rv1500/-
Rv3210c/-	(cc=0.5193)	info on Rv3210c/-
Rv0305c/PPE6	(cc=0.5174)	info on Rv0305c/PPE6
Rv3528c/-	(cc=0.5168)	info on Rv3528c/-
Rv3524/-	(cc=0.5099)	info on Rv3524/-
Rv1981c/nrdF1	(cc=0.5018)	info on Rv1981c/nrdF1
Rv0028/-	(cc=0.4889)	info on Rv0028/-
Rv0059/-	(cc=0.4872)	info on Rv0059/-

Correlation of Rv0114/gmhB with Rv1593c/-

Normalized LFCs for Rv0114/gmhB:
(description and provenance of datasets)

	Rv0114/gmhB	Rv1593c/-
Fe_supp_jason_reseq	0.718	0.043
low_pH_jason_reseq	-0.632	0.557
NO_jason_reseq	1.271	0.617
B6_jason_reseq	0.594	0.295
MHCII_jason_reseq	0.439	-0.537
Isoniazid02	-0.051	0.0
Rifampicin4	-0.046	0.831
Ethambutol3	-0.129	1.021
Meropenem3	1.923	1.105
Vancomycin16	0.409	0.337
Rv2680_day32	0.962	-1.759
H37Rv_KO_MarP	0.069	0.69
hypoxia_3wks	-0.73	-1.192
hypoxia_6wks	-0.079	-0.679
glycerol	-0.762	-1.172
cholesterol	-0.144	-1.525
AJ	0.849	-0.568
Bibs02	0.188	-1.004
Bibs02c	1.173	-1.316
BL6	1.019	1.101
BL6a	1.633	0.436
BXD01	0.578	0.931
BXD010	0.796	1.191
BXD011	2.605	2.726
BXD03	1.583	0.917
BXD04	1.206	1.905
BXD05	0.811	1.211
BXD06	1.011	1.143
BXD07	1.313	1.219
BXD08	0.994	1.04
BXD09	0.777	0.863
CAST	0.566	1.391
CCcont	0.79	0.486
DS01	0.503	-0.775
DS02	0.487	0.479
DS04	1.088	0.656
DS0c	0.544	0.152
GP01	0.688	0.496
GP02	0.101	-0.383
GP0c	0.118	0.379
NOD	1.526	-0.213
NZO	0.457	0.497
PWK	0.128	1.175
H37Rv_KO_CtpC	0.805	0.155
H37Rv_KO_CtpD	2.513	1.596
H37Rv_KO_Rv1272	1.842	-0.394
H37Rv_KO_SugABC	2.029	0.817
H37Rv_KO_MbtN	0.753	-0.855
Trans05	1.298	0.451
macrophage_unactivated	0.508	-1.139
IL1	-0.4	-0.392
Rapamycin	0.313	-0.187
Tcell	0.772	0.433
GMCSF	1.648	-0.124
IFNab	0.671	-1.116
IFNg	0.214	0.139
IFNg_GMCSF1	0.198	-0.063
Rv1432_day32	0.435	-0.669
Rv1565c_day32	-2.3	-2.267
secA2_input	-0.822	-0.808
delta_Rv3594	0.176	0.266
delta_Rv3717	0.841	0.03
delta_Rv3811	-0.052	-0.898
delta_Rv0954	0.863	0.463
PonA1	-0.166	0.214
EccD1_KO	0.115	-0.497
EspI_KO	0.083	-0.545
PE35_KO	0.344	-0.327
PPE68_KO	0.429	-0.154
glycerol2	1.023	-0.598
lignocerate	1.24	0.477
oleate	0.119	-0.658
phosphatidylcholine	1.042	0.43
acetate	0.853	0.547
glucAc	0.887	0.37
Rv0950ko	1.269	1.052
Rv1096ko	0.145	0.82
Rv3684ko	0.881	0.891
delta_otsA_trehalose	-0.281	0.081