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 Rv3240c/secA1:

update plot	correlation	link to info on gene
Rv0541c/-	(cc=0.4925)	info on Rv0541c/-
Rv1112/-	(cc=0.4653)	info on Rv1112/-
Rv2164c/-	(cc=0.4585)	info on Rv2164c/-
Rv2678c/hemE	(cc=0.4569)	info on Rv2678c/hemE
Rv3489/-	(cc=0.4348)	info on Rv3489/-
Rv1567c/-	(cc=0.4207)	info on Rv1567c/-
Rv2373c/dnaJ2	(cc=0.4164)	info on Rv2373c/dnaJ2
Rv3753c/-	(cc=0.4155)	info on Rv3753c/-
Rv3858c/gltD	(cc=0.4147)	info on Rv3858c/gltD
Rv3679/-	(cc=0.4134)	info on Rv3679/-

Correlation of Rv3240c/secA1 with Rv0541c/-

Normalized LFCs for Rv3240c/secA1:
(description and provenance of datasets)

	Rv3240c/secA1	Rv0541c/-
Fe_supp_jason_reseq	0.158	0.598
low_pH_jason_reseq	0.468	0.0
NO_jason_reseq	0.507	0.0
B6_jason_reseq	0.571	0.0
MHCII_jason_reseq	1.85	0.0
Isoniazid02	0.323	0.0
Rifampicin4	1.124	0.0
Ethambutol3	-0.32	0.0
Meropenem3	0.0	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.491	-1.683
hypoxia_3wks	-0.347	0.0
hypoxia_6wks	-0.182	0.0
glycerol	1.279	0.0
cholesterol	0.614	0.0
AJ	0.373	0.0
Bibs02	0.152	0.0
Bibs02c	0.488	0.0
BL6	0.104	0.0
BL6a	0.722	0.0
BXD01	0.825	0.0
BXD010	0.107	0.0
BXD011	0.297	0.0
BXD03	1.146	0.0
BXD04	0.999	0.0
BXD05	1.335	0.0
BXD06	0.311	0.0
BXD07	0.665	0.0
BXD08	0.31	0.0
BXD09	0.512	0.0
CAST	0.192	0.0
CCcont	0.348	0.525
DS01	1.001	0.0
DS02	0.507	0.0
DS04	0.162	0.0
DS0c	0.349	0.0
GP01	-0.09	0.0
GP02	-0.159	0.0
GP0c	-0.119	0.0
NOD	2.642	0.0
NZO	-0.182	0.0
PWK	0.163	0.0
H37Rv_KO_CtpC	-0.309	0.0
H37Rv_KO_CtpD	-0.241	0.241
H37Rv_KO_Rv1272	0.893	0.0
H37Rv_KO_SugABC	-0.189	0.0
H37Rv_KO_MbtN	-0.196	0.196
Trans05	0.393	0.0
macrophage_unactivated	0.0	0.0
IL1	0.19	0.0
Rapamycin	0.565	0.0
Tcell	0.6	0.0
GMCSF	-0.177	0.0
IFNab	0.193	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	-0.434	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-0.545	-1.882
delta_Rv3594	0.742	3.674
delta_Rv3717	1.933	3.71
delta_Rv3811	1.591	4.232
delta_Rv0954	0.178	2.348
PonA1	0.159	-1.235
EccD1_KO	-0.987	-3.887
EspI_KO	-0.856	-3.066
PE35_KO	-0.875	-2.847
PPE68_KO	-0.618	-2.409
glycerol2	-0.369	0.0
lignocerate	-0.153	0.0
oleate	0.0	0.0
phosphatidylcholine	-0.368	0.0
acetate	0.191	0.0
glucAc	0.429	0.0
Rv0950ko	0.621	-2.813
Rv1096ko	0.0	0.302
Rv3684ko	-0.377	0.327
delta_otsA_trehalose	-0.254	0.0