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 Rv3079c/-:

update plot	correlation	link to info on gene
Rv2297/-	(cc=0.4974)	info on Rv2297/-
Rv3040c/-	(cc=0.4692)	info on Rv3040c/-
Rv1168c/PPE17	(cc=0.4475)	info on Rv1168c/PPE17
Rv2410c/-	(cc=0.4343)	info on Rv2410c/-
Rv1074c/fadA3	(cc=0.4326)	info on Rv1074c/fadA3
Rv1208/gpgS	(cc=0.4307)	info on Rv1208/gpgS
Rv0853c/pdc	(cc=0.4291)	info on Rv0853c/pdc
Rv0865/mog	(cc=0.4272)	info on Rv0865/mog
Rv2624c/-	(cc=0.4272)	info on Rv2624c/-
Rv3057c/-	(cc=0.4262)	info on Rv3057c/-

Correlation of Rv3079c/- with Rv1208/gpgS

Normalized LFCs for Rv3079c/-:
(description and provenance of datasets)

	Rv3079c/-	Rv1208/gpgS
Fe_supp_jason_reseq	0.715	0.0
low_pH_jason_reseq	0.089	0.0
NO_jason_reseq	-0.234	0.0
B6_jason_reseq	0.403	0.0
MHCII_jason_reseq	-0.193	0.0
Isoniazid02	0.391	0.0
Rifampicin4	0.382	0.0
Ethambutol3	0.866	0.0
Meropenem3	0.178	0.0
Vancomycin16	0.536	0.0
Rv2680_day32	0.215	0.0
H37Rv_KO_MarP	-0.308	0.0
hypoxia_3wks	-0.315	0.0
hypoxia_6wks	-0.267	0.0
glycerol	-0.363	0.0
cholesterol	0.255	0.0
AJ	-0.647	0.0
Bibs02	0.668	0.0
Bibs02c	-0.203	0.0
BL6	-0.473	0.0
BL6a	-0.25	0.0
BXD01	0.387	0.0
BXD010	0.254	0.0
BXD011	-0.281	0.0
BXD03	-0.424	0.0
BXD04	-0.516	0.0
BXD05	-0.575	0.0
BXD06	0.11	0.0
BXD07	-0.422	0.0
BXD08	0.604	0.0
BXD09	-0.087	0.0
CAST	-0.093	0.0
CCcont	-0.794	0.149
DS01	-0.229	0.0
DS02	-0.072	0.0
DS04	-0.245	0.0
DS0c	-0.058	0.0
GP01	-0.87	0.0
GP02	0.479	0.0
GP0c	-0.622	0.0
NOD	-0.317	0.0
NZO	-1.061	0.0
PWK	0.357	0.0
H37Rv_KO_CtpC	0.607	0.0
H37Rv_KO_CtpD	0.772	0.0
H37Rv_KO_Rv1272	0.248	0.0
H37Rv_KO_SugABC	-0.118	0.0
H37Rv_KO_MbtN	-0.526	0.0
Trans05	-0.053	0.0
macrophage_unactivated	0.786	0.0
IL1	1.308	0.0
Rapamycin	0.954	0.0
Tcell	-0.186	0.0
GMCSF	0.779	0.0
IFNab	0.656	0.0
IFNg	1.323	0.0
IFNg_GMCSF1	1.471	0.0
Rv1432_day32	0.412	0.0
Rv1565c_day32	0.6	0.0
secA2_input	-1.335	-1.234
delta_Rv3594	0.283	0.0
delta_Rv3717	-0.789	0.0
delta_Rv3811	-0.706	0.0
delta_Rv0954	0.013	0.178
PonA1	-0.203	0.0
EccD1_KO	1.161	0.454
EspI_KO	2.042	1.383
PE35_KO	1.059	2.234
PPE68_KO	1.193	2.451
glycerol2	0.362	0.0
lignocerate	-0.25	0.0
oleate	0.652	0.0
phosphatidylcholine	0.581	0.0
acetate	-0.341	0.0
glucAc	-1.227	0.272
Rv0950ko	0.347	0.416
Rv1096ko	1.059	0.416
Rv3684ko	0.583	1.241
delta_otsA_trehalose	1.549	0.133