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 Rv1117/-:

update plot	correlation	link to info on gene
Rv2396/PE_PGRS41	(cc=0.5174)	info on Rv2396/PE_PGRS41
Rv1646/PE17	(cc=0.5113)	info on Rv1646/PE17
Rv3065/mmr	(cc=0.5073)	info on Rv3065/mmr
Rv3184/-	(cc=0.4719)	info on Rv3184/-
Rv3884c/eccA2	(cc=0.4637)	info on Rv3884c/eccA2
Rv0830/-	(cc=0.4427)	info on Rv0830/-
Rv2950c/fadD29	(cc=0.4345)	info on Rv2950c/fadD29
Rv2639c/-	(cc=0.4339)	info on Rv2639c/-
Rv2957/-	(cc=0.4316)	info on Rv2957/-
Rv3749c/-	(cc=0.4311)	info on Rv3749c/-

Correlation of Rv1117/- with Rv3065/mmr

Normalized LFCs for Rv1117/-:
(description and provenance of datasets)

	Rv1117/-	Rv3065/mmr
Fe_supp_jason_reseq	0.325	-0.647
low_pH_jason_reseq	0.652	-1.335
NO_jason_reseq	1.302	-0.911
B6_jason_reseq	0.628	-0.65
MHCII_jason_reseq	0.89	0.12
Isoniazid02	-1.129	-1.314
Rifampicin4	0.249	-0.301
Ethambutol3	-0.731	0.24
Meropenem3	-0.321	-1.063
Vancomycin16	-0.215	-1.149
Rv2680_day32	0.432	0.75
H37Rv_KO_MarP	-0.058	-0.042
hypoxia_3wks	-0.766	-1.113
hypoxia_6wks	-2.107	0.115
glycerol	-0.05	-0.53
cholesterol	-0.147	-0.807
AJ	1.449	0.072
Bibs02	0.948	0.209
Bibs02c	1.676	0.117
BL6	-0.049	-0.318
BL6a	0.967	-0.178
BXD01	0.889	-0.435
BXD010	0.198	0.121
BXD011	-0.323	0.109
BXD03	0.727	-0.5
BXD04	0.692	-0.514
BXD05	0.086	-0.658
BXD06	0.574	-0.417
BXD07	0.525	-1.043
BXD08	0.248	-0.713
BXD09	0.195	-0.439
CAST	0.906	0.482
CCcont	0.411	-0.46
DS01	0.385	0.684
DS02	0.11	0.315
DS04	0.429	0.055
DS0c	-0.099	-0.091
GP01	0.369	0.21
GP02	2.489	0.709
GP0c	0.316	0.091
NOD	0.251	0.656
NZO	1.211	-0.185
PWK	0.566	0.162
H37Rv_KO_CtpC	0.98	0.285
H37Rv_KO_CtpD	-0.532	0.265
H37Rv_KO_Rv1272	1.288	0.022
H37Rv_KO_SugABC	1.45	0.389
H37Rv_KO_MbtN	0.819	0.271
Trans05	0.339	0.301
macrophage_unactivated	0.095	-1.24
IL1	-1.818	-1.531
Rapamycin	-1.292	-1.344
Tcell	0.306	-1.329
GMCSF	-1.31	-1.65
IFNab	0.163	-1.013
IFNg	-1.686	-1.358
IFNg_GMCSF1	-1.1	-0.566
Rv1432_day32	-0.369	0.541
Rv1565c_day32	0.12	-1.061
secA2_input	2.365	0.512
delta_Rv3594	0.587	0.061
delta_Rv3717	0.544	-0.146
delta_Rv3811	0.132	0.03
delta_Rv0954	0.464	0.193
PonA1	0.542	-0.314
EccD1_KO	0.96	0.434
EspI_KO	1.694	1.483
PE35_KO	1.89	0.298
PPE68_KO	1.878	0.035
glycerol2	1.418	0.551
lignocerate	0.784	0.491
oleate	1.448	0.346
phosphatidylcholine	0.98	0.728
acetate	0.741	-0.204
glucAc	0.748	0.637
Rv0950ko	-0.425	0.47
Rv1096ko	-0.495	-0.106
Rv3684ko	-0.57	0.029
delta_otsA_trehalose	-1.122	-0.588