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 Rv2434c/-:

update plot	correlation	link to info on gene
Rv2455c/-	(cc=0.5506)	info on Rv2455c/-
Rv2454c/-	(cc=0.4947)	info on Rv2454c/-
Rv2393/che1	(cc=0.4817)	info on Rv2393/che1
Rv1208/gpgS	(cc=0.4796)	info on Rv1208/gpgS
Rv2282c/-	(cc=0.4689)	info on Rv2282c/-
Rv2847c/cysG	(cc=0.445)	info on Rv2847c/cysG
Rv2381c/mbtD	(cc=0.4385)	info on Rv2381c/mbtD
Rv2432c/-	(cc=0.4379)	info on Rv2432c/-
Rv2840c/-	(cc=0.4309)	info on Rv2840c/-
Rv2761c/hsdS	(cc=0.4269)	info on Rv2761c/hsdS

Correlation of Rv2434c/- with Rv2393/che1

Normalized LFCs for Rv2434c/-:
(description and provenance of datasets)

	Rv2434c/-	Rv2393/che1
Fe_supp_jason_reseq	-0.598	0.0
low_pH_jason_reseq	0.463	0.0
NO_jason_reseq	-0.302	0.0
B6_jason_reseq	0.586	0.0
MHCII_jason_reseq	0.399	0.0
Isoniazid02	1.336	2.802
Rifampicin4	0.087	0.49
Ethambutol3	-0.122	-0.392
Meropenem3	0.147	-0.386
Vancomycin16	0.247	-0.546
Rv2680_day32	-0.5	0.0
H37Rv_KO_MarP	0.291	-0.195
hypoxia_3wks	-0.259	0.0
hypoxia_6wks	0.213	0.0
glycerol	-0.512	0.0
cholesterol	-1.026	0.0
AJ	-0.839	0.0
Bibs02	0.579	0.0
Bibs02c	0.561	0.0
BL6	0.758	0.0
BL6a	0.063	0.0
BXD01	0.265	0.0
BXD010	0.294	0.0
BXD011	0.079	0.0
BXD03	-0.52	0.0
BXD04	-0.476	0.0
BXD05	0.238	0.0
BXD06	0.219	0.0
BXD07	-0.295	0.0
BXD08	0.18	0.0
BXD09	0.69	0.0
CAST	0.037	0.0
CCcont	0.4	0.149
DS01	0.775	0.0
DS02	1.744	0.0
DS04	1.244	0.0
DS0c	0.859	0.0
GP01	0.358	0.0
GP02	0.089	0.0
GP0c	-0.47	0.0
NOD	0.036	0.0
NZO	-0.273	0.0
PWK	-0.199	0.0
H37Rv_KO_CtpC	0.552	0.0
H37Rv_KO_CtpD	0.0	0.0
H37Rv_KO_Rv1272	-0.791	0.0
H37Rv_KO_SugABC	-0.583	0.0
H37Rv_KO_MbtN	-0.326	0.0
Trans05	-0.386	0.0
macrophage_unactivated	0.126	0.0
IL1	0.231	0.0
Rapamycin	0.0	0.0
Tcell	0.495	0.0
GMCSF	0.206	0.0
IFNab	-0.314	0.0
IFNg	0.775	0.0
IFNg_GMCSF1	0.361	0.0
Rv1432_day32	-0.679	0.0
Rv1565c_day32	0.051	0.0
secA2_input	-1.99	-0.847
delta_Rv3594	-0.953	0.0
delta_Rv3717	-0.598	0.0
delta_Rv3811	-0.706	0.0
delta_Rv0954	-0.482	0.34
PonA1	0.457	0.437
EccD1_KO	0.329	0.0
EspI_KO	1.258	0.394
PE35_KO	1.569	2.917
PPE68_KO	1.568	0.841
glycerol2	0.137	0.0
lignocerate	0.357	0.0
oleate	-0.213	0.0
phosphatidylcholine	-0.028	0.0
acetate	0.346	0.0
glucAc	0.141	0.392
Rv0950ko	-0.522	-0.971
Rv1096ko	-0.217	-0.971
Rv3684ko	-0.075	-0.327
delta_otsA_trehalose	-0.214	-0.366