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 Rv0235c/-:

update plot	correlation	link to info on gene
Rv1058/fadD14	(cc=0.5951)	info on Rv1058/fadD14
Rv0973c/accA2	(cc=0.5835)	info on Rv0973c/accA2
Rv3148/nuoD	(cc=0.5759)	info on Rv3148/nuoD
Rv1831/-	(cc=0.5649)	info on Rv1831/-
Rv3112/moaD1	(cc=0.5599)	info on Rv3112/moaD1
Rv0742/PE_PGRS8	(cc=0.5599)	info on Rv0742/PE_PGRS8
Rv1914c/-	(cc=0.5571)	info on Rv1914c/-
Rv3511/PE_PGRS55	(cc=0.5471)	info on Rv3511/PE_PGRS55
Rv3176c/mesT	(cc=0.5412)	info on Rv3176c/mesT
Rv0644c/mmaA2	(cc=0.541)	info on Rv0644c/mmaA2

Correlation of Rv0235c/- with Rv1914c/-

Normalized LFCs for Rv0235c/-:
(description and provenance of datasets)

	Rv0235c/-	Rv1914c/-
Fe_supp_jason_reseq	-0.783	0.174
low_pH_jason_reseq	-0.204	-1.084
NO_jason_reseq	0.0	-0.026
B6_jason_reseq	-0.687	-0.392
MHCII_jason_reseq	-0.63	-0.923
Isoniazid02	0.164	0.044
Rifampicin4	0.0	-0.276
Ethambutol3	0.035	0.08
Meropenem3	0.035	0.328
Vancomycin16	0.0	0.157
Rv2680_day32	0.105	0.221
H37Rv_KO_MarP	0.155	-0.155
hypoxia_3wks	0.191	0.778
hypoxia_6wks	-0.443	-0.109
glycerol	0.075	-0.742
cholesterol	-0.055	-0.967
AJ	0.086	-0.58
Bibs02	-1.13	-0.672
Bibs02c	0.039	0.138
BL6	1.27	0.906
BL6a	1.072	1.72
BXD01	1.126	1.023
BXD010	0.904	0.909
BXD011	0.508	1.315
BXD03	1.42	1.509
BXD04	1.098	0.999
BXD05	0.447	1.235
BXD06	0.863	0.98
BXD07	1.406	1.029
BXD08	0.874	1.121
BXD09	0.578	1.031
CAST	0.205	0.087
CCcont	1.15	0.383
DS01	0.044	-0.9
DS02	-0.082	-1.534
DS04	0.394	0.36
DS0c	-0.041	-1.409
GP01	1.319	1.159
GP02	2.076	1.46
GP0c	0.788	0.41
NOD	0.866	0.626
NZO	0.212	0.038
PWK	0.571	-0.516
H37Rv_KO_CtpC	1.221	0.288
H37Rv_KO_CtpD	-0.661	0.372
H37Rv_KO_Rv1272	0.451	1.048
H37Rv_KO_SugABC	1.891	1.601
H37Rv_KO_MbtN	0.462	0.574
Trans05	1.231	1.927
macrophage_unactivated	0.805	0.29
IL1	0.0	0.252
Rapamycin	-0.592	-1.028
Tcell	0.209	-0.424
GMCSF	0.708	0.169
IFNab	-0.756	-0.157
IFNg	-0.775	0.096
IFNg_GMCSF1	-0.666	0.223
Rv1432_day32	1.25	-0.446
Rv1565c_day32	0.0	0.684
secA2_input	-0.031	-1.794
delta_Rv3594	0.909	1.834
delta_Rv3717	0.893	-0.311
delta_Rv3811	0.721	1.072
delta_Rv0954	0.699	0.443
PonA1	0.278	0.569
EccD1_KO	0.0	-0.184
EspI_KO	-0.419	-0.841
PE35_KO	-0.28	0.933
PPE68_KO	0.099	1.232
glycerol2	1.1	0.385
lignocerate	0.956	-0.239
oleate	0.719	0.39
phosphatidylcholine	0.634	0.676
acetate	0.459	-0.598
glucAc	1.092	-0.65
Rv0950ko	-0.292	-0.259
Rv1096ko	-0.048	-0.075
Rv3684ko	-0.373	0.344
delta_otsA_trehalose	-1.372	-0.138