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 Rv2662/-:

update plot	correlation	link to info on gene
Rv2911/dacB2	(cc=0.4301)	info on Rv2911/dacB2
Rv0516c/-	(cc=0.3774)	info on Rv0516c/-
Rv2148c/-	(cc=0.356)	info on Rv2148c/-
Rv1477/ripA	(cc=0.3539)	info on Rv1477/ripA
Rv3856c/-	(cc=0.3485)	info on Rv3856c/-
Rv1527c/pks5	(cc=0.3478)	info on Rv1527c/pks5
Rv1089/PE10	(cc=0.3455)	info on Rv1089/PE10
Rv0969/ctpV	(cc=0.3432)	info on Rv0969/ctpV
Rv0630c/recB	(cc=0.3416)	info on Rv0630c/recB
Rv1961/-	(cc=0.3411)	info on Rv1961/-

Correlation of Rv2662/- with Rv3856c/-

Normalized LFCs for Rv2662/-:
(description and provenance of datasets)

	Rv2662/-	Rv3856c/-
Fe_supp_jason_reseq	1.86	0.043
low_pH_jason_reseq	-0.547	1.762
NO_jason_reseq	-0.05	-0.375
B6_jason_reseq	-0.057	0.185
MHCII_jason_reseq	-1.027	0.255
Isoniazid02	0.009	-0.201
Rifampicin4	-0.068	0.433
Ethambutol3	-0.185	0.275
Meropenem3	-0.165	0.547
Vancomycin16	0.684	0.172
Rv2680_day32	-0.228	-1.406
H37Rv_KO_MarP	0.862	-0.167
hypoxia_3wks	-0.124	-0.475
hypoxia_6wks	0.077	-0.305
glycerol	-0.161	-0.59
cholesterol	-0.61	-0.546
AJ	0.844	0.324
Bibs02	0.984	0.139
Bibs02c	0.556	0.324
BL6	0.161	-0.294
BL6a	0.818	0.215
BXD01	-0.368	-0.12
BXD010	0.495	0.169
BXD011	-0.021	0.148
BXD03	0.093	-0.164
BXD04	-0.511	0.612
BXD05	1.146	-0.393
BXD06	0.218	0.165
BXD07	-0.015	0.036
BXD08	0.065	0.552
BXD09	0.293	-0.738
CAST	-1.086	0.873
CCcont	0.127	-0.094
DS01	0.84	0.85
DS02	1.084	0.369
DS04	2.195	2.194
DS0c	0.343	0.148
GP01	3.083	1.528
GP02	0.266	2.115
GP0c	1.181	0.766
NOD	-1.261	0.739
NZO	1.932	0.886
PWK	0.033	0.568
H37Rv_KO_CtpC	0.683	0.014
H37Rv_KO_CtpD	-0.414	-0.952
H37Rv_KO_Rv1272	0.127	0.107
H37Rv_KO_SugABC	0.865	0.542
H37Rv_KO_MbtN	1.546	1.14
Trans05	-0.823	-0.559
macrophage_unactivated	1.272	1.171
IL1	0.724	-1.02
Rapamycin	-0.853	-0.675
Tcell	0.274	-0.094
GMCSF	-0.671	-0.536
IFNab	0.889	0.577
IFNg	0.224	-0.2
IFNg_GMCSF1	1.04	-0.434
Rv1432_day32	0.0	0.342
Rv1565c_day32	-1.657	-0.065
secA2_input	0.299	-0.094
delta_Rv3594	0.642	-0.333
delta_Rv3717	0.922	0.059
delta_Rv3811	0.916	0.816
delta_Rv0954	0.129	0.388
PonA1	-0.669	-0.042
EccD1_KO	0.52	0.658
EspI_KO	0.111	-0.402
PE35_KO	1.698	0.204
PPE68_KO	2.262	-0.086
glycerol2	0.193	-0.149
lignocerate	1.019	0.068
oleate	-2.066	-0.065
phosphatidylcholine	0.258	-0.384
acetate	0.289	0.0
glucAc	0.333	-0.746
Rv0950ko	0.844	0.501
Rv1096ko	1.858	0.875
Rv3684ko	1.611	0.838
delta_otsA_trehalose	0.957	-0.128