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 Rv1010/ksgA:

update plot	correlation	link to info on gene
Rv3193c/-	(cc=0.7255)	info on Rv3193c/-
Rv2169c/-	(cc=0.6961)	info on Rv2169c/-
Rv2909c/rpsP	(cc=0.6744)	info on Rv2909c/rpsP
Rv2535c/pepQ	(cc=0.6603)	info on Rv2535c/pepQ
Rv0003/recF	(cc=0.6505)	info on Rv0003/recF
Rv1638/uvrA	(cc=0.6491)	info on Rv1638/uvrA
Rv2518c/ldtB	(cc=0.6422)	info on Rv2518c/ldtB
Rv3228/-	(cc=0.6348)	info on Rv3228/-
Rv2342/-	(cc=0.6119)	info on Rv2342/-
Rv2737c/recA	(cc=0.6051)	info on Rv2737c/recA

Correlation of Rv1010/ksgA with Rv2909c/rpsP

Normalized LFCs for Rv1010/ksgA:
(description and provenance of datasets)

	Rv1010/ksgA	Rv2909c/rpsP
Fe_supp_jason_reseq	1.796	0.415
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.362	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.135
Isoniazid02	-0.885	0.0
Rifampicin4	-2.708	0.0
Ethambutol3	2.486	0.461
Meropenem3	-0.497	0.701
Vancomycin16	0.95	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	2.654	1.573
hypoxia_3wks	-1.388	-0.55
hypoxia_6wks	-0.727	-0.288
glycerol	0.992	0.554
cholesterol	1.558	0.0
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.399	0.0
BL6	0.125	0.0
BL6a	0.198	0.198
BXD01	0.13	0.0
BXD010	0.0	0.0
BXD011	0.243	0.0
BXD03	0.573	0.0
BXD04	0.124	0.0
BXD05	0.135	0.0
BXD06	0.469	0.0
BXD07	0.264	0.0
BXD08	0.253	0.0
BXD09	0.14	0.0
CAST	0.0	0.0
CCcont	2.822	0.149
DS01	0.236	0.0
DS02	0.0	0.0
DS04	0.194	0.0
DS0c	0.217	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.162	0.0
H37Rv_KO_CtpD	0.445	0.0
H37Rv_KO_Rv1272	0.387	0.0
H37Rv_KO_SugABC	0.55	0.0
H37Rv_KO_MbtN	0.747	0.0
Trans05	0.249	0.0
macrophage_unactivated	0.83	0.0
IL1	0.409	0.0
Rapamycin	0.0	0.0
Tcell	0.857	0.0
GMCSF	0.0	0.0
IFNab	0.417	0.0
IFNg	0.369	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	-0.18	0.0
Rv1565c_day32	0.199	0.0
secA2_input	-0.611	-0.322
delta_Rv3594	-0.096	0.788
delta_Rv3717	-0.763	-0.61
delta_Rv3811	-0.596	-0.518
delta_Rv0954	-0.226	0.129
PonA1	0.509	-0.402
EccD1_KO	-0.329	-0.454
EspI_KO	0.633	-0.394
PE35_KO	2.234	-0.403
PPE68_KO	1.661	0.0
glycerol2	-2.36	-1.96
lignocerate	-2.642	-1.87
oleate	-2.704	-2.178
phosphatidylcholine	-2.846	-2.151
acetate	-0.818	-0.085
glucAc	-0.462	-1.588
Rv0950ko	-0.458	0.38
Rv1096ko	-0.362	-0.416
Rv3684ko	-0.937	-0.452
delta_otsA_trehalose	0.126	0.0