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 Rv0973c/accA2

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

	Rv0235c/-	Rv0973c/accA2
Fe_supp_jason_reseq	-0.783	-2.087
low_pH_jason_reseq	-0.204	0.117
NO_jason_reseq	0.0	0.446
B6_jason_reseq	-0.687	0.078
MHCII_jason_reseq	-0.63	-1.206
Isoniazid02	0.164	0.221
Rifampicin4	0.0	0.539
Ethambutol3	0.035	0.125
Meropenem3	0.035	0.294
Vancomycin16	0.0	0.0
Rv2680_day32	0.105	-0.628
H37Rv_KO_MarP	0.155	0.0
hypoxia_3wks	0.191	0.339
hypoxia_6wks	-0.443	-0.188
glycerol	0.075	-0.607
cholesterol	-0.055	-0.203
AJ	0.086	-0.698
Bibs02	-1.13	-0.898
Bibs02c	0.039	-0.141
BL6	1.27	1.322
BL6a	1.072	0.462
BXD01	1.126	1.467
BXD010	0.904	2.103
BXD011	0.508	1.253
BXD03	1.42	0.79
BXD04	1.098	0.469
BXD05	0.447	1.06
BXD06	0.863	1.443
BXD07	1.406	1.889
BXD08	0.874	1.814
BXD09	0.578	0.873
CAST	0.205	0.145
CCcont	1.15	1.35
DS01	0.044	-0.33
DS02	-0.082	0.507
DS04	0.394	-0.131
DS0c	-0.041	0.721
GP01	1.319	0.461
GP02	2.076	0.486
GP0c	0.788	0.711
NOD	0.866	1.139
NZO	0.212	0.358
PWK	0.571	0.458
H37Rv_KO_CtpC	1.221	1.678
H37Rv_KO_CtpD	-0.661	-0.177
H37Rv_KO_Rv1272	0.451	2.196
H37Rv_KO_SugABC	1.891	1.023
H37Rv_KO_MbtN	0.462	0.603
Trans05	1.231	1.686
macrophage_unactivated	0.805	0.275
IL1	0.0	0.62
Rapamycin	-0.592	0.396
Tcell	0.209	0.283
GMCSF	0.708	0.655
IFNab	-0.756	0.0
IFNg	-0.775	0.559
IFNg_GMCSF1	-0.666	0.534
Rv1432_day32	1.25	0.705
Rv1565c_day32	0.0	0.046
secA2_input	-0.031	-0.678
delta_Rv3594	0.909	0.713
delta_Rv3717	0.893	0.317
delta_Rv3811	0.721	0.617
delta_Rv0954	0.699	0.602
PonA1	0.278	0.0
EccD1_KO	0.0	-0.582
EspI_KO	-0.419	0.305
PE35_KO	-0.28	0.461
PPE68_KO	0.099	0.342
glycerol2	1.1	0.27
lignocerate	0.956	0.035
oleate	0.719	0.61
phosphatidylcholine	0.634	0.443
acetate	0.459	-0.258
glucAc	1.092	-0.229
Rv0950ko	-0.292	-1.251
Rv1096ko	-0.048	0.389
Rv3684ko	-0.373	0.557
delta_otsA_trehalose	-1.372	-0.4