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 Rv1707/-:

update plot	correlation	link to info on gene
Rv0231/fadE4	(cc=0.5246)	info on Rv0231/fadE4
Rv0268c/-	(cc=0.4532)	info on Rv0268c/-
Rv0588/yrbE2B	(cc=0.4475)	info on Rv0588/yrbE2B
Rv3011c/gatA	(cc=0.4356)	info on Rv3011c/gatA
Rv3437/-	(cc=0.431)	info on Rv3437/-
Rv0145/-	(cc=0.4145)	info on Rv0145/-
Rv0905/echA6	(cc=0.4125)	info on Rv0905/echA6
Rv3675/-	(cc=0.4109)	info on Rv3675/-
Rv3435c/-	(cc=0.4075)	info on Rv3435c/-
Rv2594c/ruvC	(cc=0.4058)	info on Rv2594c/ruvC

Correlation of Rv1707/- with Rv3675/-

Normalized LFCs for Rv1707/-:
(description and provenance of datasets)

	Rv1707/-	Rv3675/-
Fe_supp_jason_reseq	-0.251	0.802
low_pH_jason_reseq	-0.564	-1.7
NO_jason_reseq	1.901	0.743
B6_jason_reseq	0.21	-0.368
MHCII_jason_reseq	0.458	0.12
Isoniazid02	-0.096	0.37
Rifampicin4	-2.166	-1.432
Ethambutol3	-1.131	1.859
Meropenem3	-0.491	-0.842
Vancomycin16	-2.258	-0.578
Rv2680_day32	0.083	-1.557
H37Rv_KO_MarP	0.068	0.919
hypoxia_3wks	-0.618	-1.424
hypoxia_6wks	-1.62	-1.201
glycerol	0.102	0.66
cholesterol	-0.959	-0.749
AJ	1.298	0.071
Bibs02	0.279	-0.215
Bibs02c	-0.103	-0.54
BL6	-0.438	0.578
BL6a	0.29	0.794
BXD01	-0.284	0.865
BXD010	0.559	1.314
BXD011	0.498	0.573
BXD03	0.15	0.839
BXD04	-0.051	0.918
BXD05	0.339	1.307
BXD06	0.083	1.145
BXD07	0.287	0.924
BXD08	0.203	1.04
BXD09	0.441	0.715
CAST	0.574	0.612
CCcont	-0.371	1.172
DS01	-0.493	1.138
DS02	-1.007	1.459
DS04	-0.32	-0.339
DS0c	-0.135	0.347
GP01	0.307	0.881
GP02	0.594	1.938
GP0c	0.076	0.888
NOD	0.28	0.672
NZO	0.655	0.597
PWK	0.988	1.353
H37Rv_KO_CtpC	-0.625	-0.168
H37Rv_KO_CtpD	0.495	0.061
H37Rv_KO_Rv1272	0.13	0.375
H37Rv_KO_SugABC	-0.241	0.469
H37Rv_KO_MbtN	0.477	0.327
Trans05	-0.393	-0.307
macrophage_unactivated	-0.877	1.209
IL1	0.288	0.765
Rapamycin	-0.911	-0.267
Tcell	0.033	0.57
GMCSF	-0.333	0.573
IFNab	-0.783	0.23
IFNg	0.82	1.251
IFNg_GMCSF1	0.179	0.666
Rv1432_day32	-0.97	0.164
Rv1565c_day32	-0.141	-0.452
secA2_input	0.0	-0.218
delta_Rv3594	0.0	-0.515
delta_Rv3717	-0.059	-0.541
delta_Rv3811	-0.07	0.058
delta_Rv0954	1.156	0.154
PonA1	0.986	1.21
EccD1_KO	-0.789	-0.605
EspI_KO	-1.454	-0.867
PE35_KO	-1.388	0.058
PPE68_KO	-0.346	-0.662
glycerol2	0.377	0.545
lignocerate	-0.511	0.656
oleate	0.142	0.176
phosphatidylcholine	1.518	0.641
acetate	0.073	-0.17
glucAc	-0.207	-0.329
Rv0950ko	1.288	0.579
Rv1096ko	0.618	0.317
Rv3684ko	1.009	0.383
delta_otsA_trehalose	0.135	1.136