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 Rv1165/typA:

update plot	correlation	link to info on gene
Rv3920c/-	(cc=0.5499)	info on Rv3920c/-
Rv2983/-	(cc=0.535)	info on Rv2983/-
Rv3041c/-	(cc=0.5266)	info on Rv3041c/-
Rv2125/-	(cc=0.5228)	info on Rv2125/-
Rv2831/echA16	(cc=0.5129)	info on Rv2831/echA16
Rv2404c/lepA	(cc=0.4708)	info on Rv2404c/lepA
Rv2672/-	(cc=0.4557)	info on Rv2672/-
Rv3557c/-	(cc=0.4503)	info on Rv3557c/-
Rv3228/-	(cc=0.4443)	info on Rv3228/-
Rv2733c/-	(cc=0.4418)	info on Rv2733c/-

Correlation of Rv1165/typA with Rv2125/-

Normalized LFCs for Rv1165/typA:
(description and provenance of datasets)

	Rv1165/typA	Rv2125/-
Fe_supp_jason_reseq	-0.191	0.845
low_pH_jason_reseq	-0.015	-0.231
NO_jason_reseq	0.764	-0.11
B6_jason_reseq	0.078	0.428
MHCII_jason_reseq	0.896	0.874
Isoniazid02	1.302	1.013
Rifampicin4	0.818	-0.171
Ethambutol3	0.083	0.06
Meropenem3	-0.504	0.159
Vancomycin16	0.825	-0.106
Rv2680_day32	-0.932	-0.055
H37Rv_KO_MarP	1.116	0.876
hypoxia_3wks	0.108	0.0
hypoxia_6wks	-0.958	-0.299
glycerol	1.033	1.122
cholesterol	-0.015	0.722
AJ	0.182	0.368
Bibs02	-0.568	-0.371
Bibs02c	-0.382	0.394
BL6	-0.653	-1.865
BL6a	-0.397	-0.342
BXD01	-0.344	-1.648
BXD010	-0.13	-1.35
BXD011	-0.136	-1.534
BXD03	-0.861	-1.12
BXD04	0.392	-1.647
BXD05	-0.455	-0.946
BXD06	-0.26	-1.222
BXD07	-0.509	-1.3
BXD08	0.097	-1.139
BXD09	-0.408	-1.068
CAST	-0.462	-0.661
CCcont	-0.281	-1.205
DS01	0.397	0.022
DS02	-0.282	-0.391
DS04	-0.09	0.475
DS0c	0.086	-0.035
GP01	-0.355	0.67
GP02	0.033	0.046
GP0c	-0.301	0.522
NOD	-0.89	0.145
NZO	-0.821	-0.539
PWK	0.438	-0.826
H37Rv_KO_CtpC	-0.297	-1.043
H37Rv_KO_CtpD	-0.201	-1.512
H37Rv_KO_Rv1272	-0.601	-1.109
H37Rv_KO_SugABC	0.2	0.948
H37Rv_KO_MbtN	1.249	0.311
Trans05	-0.38	-1.4
macrophage_unactivated	0.025	0.249
IL1	0.154	-0.024
Rapamycin	0.092	0.43
Tcell	0.049	-0.971
GMCSF	0.309	0.042
IFNab	0.248	0.239
IFNg	0.198	-0.224
IFNg_GMCSF1	0.025	0.575
Rv1432_day32	-0.841	0.095
Rv1565c_day32	0.308	0.485
secA2_input	0.045	0.106
delta_Rv3594	0.75	0.965
delta_Rv3717	0.43	1.072
delta_Rv3811	0.886	1.184
delta_Rv0954	0.373	1.26
PonA1	0.738	0.965
EccD1_KO	-0.056	0.562
EspI_KO	0.26	0.502
PE35_KO	0.359	0.16
PPE68_KO	-0.029	0.474
glycerol2	-1.391	-1.033
lignocerate	-0.374	-0.669
oleate	-1.202	-0.88
phosphatidylcholine	-0.462	-0.819
acetate	-0.387	0.318
glucAc	-0.062	0.0
Rv0950ko	-0.075	-0.151
Rv1096ko	0.386	0.106
Rv3684ko	-0.4	-0.747
delta_otsA_trehalose	0.429	0.132