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 Rv0923c/-:

update plot	correlation	link to info on gene
Rv0853c/pdc	(cc=0.4748)	info on Rv0853c/pdc
Rv0388c/PPE9	(cc=0.445)	info on Rv0388c/PPE9
Rv1365c/rsfA	(cc=0.4246)	info on Rv1365c/rsfA
Rv1615/-	(cc=0.4176)	info on Rv1615/-
Rv3141/fadB4	(cc=0.4162)	info on Rv3141/fadB4
Rv1414/-	(cc=0.4148)	info on Rv1414/-
Rv0576/-	(cc=0.4014)	info on Rv0576/-
Rv1418/lprH	(cc=0.3994)	info on Rv1418/lprH
Rv2251/-	(cc=0.3969)	info on Rv2251/-
Rv3398c/idsA1	(cc=0.3952)	info on Rv3398c/idsA1

Correlation of Rv0923c/- with Rv0853c/pdc

Normalized LFCs for Rv0923c/-:
(description and provenance of datasets)

	Rv0923c/-	Rv0853c/pdc
Fe_supp_jason_reseq	-0.59	-0.346
low_pH_jason_reseq	0.37	-0.278
NO_jason_reseq	-0.635	-1.189
B6_jason_reseq	-0.28	0.341
MHCII_jason_reseq	-0.508	0.358
Isoniazid02	0.055	0.137
Rifampicin4	0.333	0.255
Ethambutol3	0.524	0.663
Meropenem3	0.562	0.089
Vancomycin16	0.135	0.141
Rv2680_day32	0.36	-0.592
H37Rv_KO_MarP	0.141	-0.135
hypoxia_3wks	0.0	-0.407
hypoxia_6wks	-0.111	0.238
glycerol	-0.408	-0.35
cholesterol	0.18	-0.408
AJ	0.365	-0.632
Bibs02	0.332	-0.196
Bibs02c	-0.279	-0.797
BL6	0.295	-0.283
BL6a	0.099	-0.088
BXD01	0.743	0.064
BXD010	0.431	0.35
BXD011	0.27	0.197
BXD03	0.526	-0.04
BXD04	0.566	0.222
BXD05	0.796	0.33
BXD06	0.443	0.304
BXD07	0.473	0.161
BXD08	0.646	0.039
BXD09	0.561	-0.196
CAST	0.227	-0.878
CCcont	0.519	-0.032
DS01	0.585	0.366
DS02	0.369	0.581
DS04	1.179	0.594
DS0c	0.844	-0.08
GP01	-0.605	-1.223
GP02	0.9	-0.166
GP0c	-0.449	-0.442
NOD	0.973	1.1
NZO	0.459	-0.328
PWK	0.0	-0.117
H37Rv_KO_CtpC	-0.3	-0.035
H37Rv_KO_CtpD	0.009	0.421
H37Rv_KO_Rv1272	-0.503	0.164
H37Rv_KO_SugABC	0.425	0.225
H37Rv_KO_MbtN	-0.128	0.386
Trans05	-0.163	0.863
macrophage_unactivated	1.433	0.903
IL1	0.572	0.543
Rapamycin	1.068	0.384
Tcell	0.733	-0.029
GMCSF	1.288	0.261
IFNab	0.822	0.245
IFNg	0.537	0.147
IFNg_GMCSF1	1.449	1.178
Rv1432_day32	0.948	0.287
Rv1565c_day32	-0.158	0.077
secA2_input	0.384	-0.363
delta_Rv3594	0.594	0.54
delta_Rv3717	0.074	-0.083
delta_Rv3811	-0.226	0.4
delta_Rv0954	0.287	0.017
PonA1	0.184	-0.015
EccD1_KO	0.526	0.204
EspI_KO	0.588	1.084
PE35_KO	-0.155	0.268
PPE68_KO	-0.256	0.72
glycerol2	0.128	0.31
lignocerate	0.38	0.723
oleate	0.468	0.169
phosphatidylcholine	0.462	0.132
acetate	-0.878	-0.598
glucAc	-0.554	-0.154
Rv0950ko	-0.042	-0.567
Rv1096ko	1.149	0.419
Rv3684ko	0.386	0.147
delta_otsA_trehalose	-0.603	-0.022