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 Rv0063/-:

update plot	correlation	link to info on gene
Rv1675c/cmr	(cc=0.5603)	info on Rv1675c/cmr
Rv0669c/-	(cc=0.5197)	info on Rv0669c/-
Rv0338c/-	(cc=0.5024)	info on Rv0338c/-
Rv3283/sseA	(cc=0.4817)	info on Rv3283/sseA
Rv2268c/cyp128	(cc=0.4799)	info on Rv2268c/cyp128
Rv1371/-	(cc=0.4686)	info on Rv1371/-
Rv2431c/PE25	(cc=0.4568)	info on Rv2431c/PE25
Rv3509c/ilvX	(cc=0.4437)	info on Rv3509c/ilvX
Rv3154/nuoJ	(cc=0.4374)	info on Rv3154/nuoJ
Rv3529c/-	(cc=0.435)	info on Rv3529c/-

Correlation of Rv0063/- with Rv0669c/-

Normalized LFCs for Rv0063/-:
(description and provenance of datasets)

	Rv0063/-	Rv0669c/-
Fe_supp_jason_reseq	-0.568	-0.156
low_pH_jason_reseq	-0.172	-0.582
NO_jason_reseq	-0.026	0.039
B6_jason_reseq	0.872	0.331
MHCII_jason_reseq	0.139	0.163
Isoniazid02	-0.228	0.247
Rifampicin4	0.0	0.0
Ethambutol3	-0.134	1.07
Meropenem3	0.037	0.492
Vancomycin16	0.218	-0.019
Rv2680_day32	-0.874	0.483
H37Rv_KO_MarP	0.775	0.344
hypoxia_3wks	-0.805	-0.231
hypoxia_6wks	-0.24	0.092
glycerol	1.176	0.445
cholesterol	2.914	3.252
AJ	0.788	0.279
Bibs02	-0.029	0.317
Bibs02c	0.587	-0.03
BL6	0.621	-0.03
BL6a	0.43	-0.135
BXD01	-0.098	0.134
BXD010	0.261	-0.056
BXD011	0.587	0.12
BXD03	0.756	0.318
BXD04	0.354	0.164
BXD05	0.599	0.121
BXD06	0.043	0.155
BXD07	0.148	0.013
BXD08	0.011	0.209
BXD09	-0.046	-0.161
CAST	0.516	0.237
CCcont	0.07	-0.276
DS01	1.136	0.212
DS02	0.726	0.386
DS04	1.318	0.513
DS0c	0.662	0.138
GP01	0.201	0.31
GP02	-0.748	-0.395
GP0c	-0.251	-0.135
NOD	1.36	0.251
NZO	0.446	0.247
PWK	0.924	0.269
H37Rv_KO_CtpC	0.0	-0.127
H37Rv_KO_CtpD	-0.283	0.199
H37Rv_KO_Rv1272	-0.233	0.534
H37Rv_KO_SugABC	0.942	1.096
H37Rv_KO_MbtN	0.276	-0.03
Trans05	-0.548	-0.076
macrophage_unactivated	-0.363	-0.174
IL1	-0.053	-0.486
Rapamycin	-0.835	-0.718
Tcell	-0.606	0.042
GMCSF	0.166	-0.09
IFNab	0.0	-0.405
IFNg	-0.048	-0.521
IFNg_GMCSF1	-0.088	-0.493
Rv1432_day32	-0.089	0.183
Rv1565c_day32	0.351	-0.22
secA2_input	0.095	-1.021
delta_Rv3594	-0.159	-0.32
delta_Rv3717	-0.458	-0.322
delta_Rv3811	-0.607	-0.103
delta_Rv0954	0.522	-0.91
PonA1	0.658	-0.372
EccD1_KO	-0.178	0.385
EspI_KO	-0.317	0.642
PE35_KO	0.271	0.076
PPE68_KO	0.266	0.163
glycerol2	0.048	0.815
lignocerate	0.664	0.919
oleate	-1.212	0.333
phosphatidylcholine	-0.253	0.944
acetate	0.484	0.532
glucAc	0.575	0.573
Rv0950ko	0.425	0.265
Rv1096ko	0.392	0.066
Rv3684ko	0.747	0.265
delta_otsA_trehalose	-0.535	-1.542