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 Rv0742/PE_PGRS8

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

	Rv0235c/-	Rv0742/PE_PGRS8
Fe_supp_jason_reseq	-0.783	-1.888
low_pH_jason_reseq	-0.204	0.562
NO_jason_reseq	0.0	-0.538
B6_jason_reseq	-0.687	-1.831
MHCII_jason_reseq	-0.63	-2.072
Isoniazid02	0.164	-0.065
Rifampicin4	0.0	1.616
Ethambutol3	0.035	-0.044
Meropenem3	0.035	0.386
Vancomycin16	0.0	-0.024
Rv2680_day32	0.105	0.605
H37Rv_KO_MarP	0.155	0.477
hypoxia_3wks	0.191	0.833
hypoxia_6wks	-0.443	-1.088
glycerol	0.075	0.045
cholesterol	-0.055	-0.366
AJ	0.086	0.128
Bibs02	-1.13	-0.36
Bibs02c	0.039	0.799
BL6	1.27	1.464
BL6a	1.072	1.39
BXD01	1.126	1.329
BXD010	0.904	0.519
BXD011	0.508	1.026
BXD03	1.42	1.328
BXD04	1.098	0.0
BXD05	0.447	1.827
BXD06	0.863	0.571
BXD07	1.406	0.83
BXD08	0.874	1.234
BXD09	0.578	1.298
CAST	0.205	1.053
CCcont	1.15	1.218
DS01	0.044	0.587
DS02	-0.082	0.21
DS04	0.394	0.266
DS0c	-0.041	-0.341
GP01	1.319	2.262
GP02	2.076	1.611
GP0c	0.788	1.126
NOD	0.866	-0.6
NZO	0.212	-0.448
PWK	0.571	0.573
H37Rv_KO_CtpC	1.221	1.092
H37Rv_KO_CtpD	-0.661	0.494
H37Rv_KO_Rv1272	0.451	0.94
H37Rv_KO_SugABC	1.891	0.915
H37Rv_KO_MbtN	0.462	0.937
Trans05	1.231	1.328
macrophage_unactivated	0.805	0.922
IL1	0.0	0.581
Rapamycin	-0.592	0.703
Tcell	0.209	0.766
GMCSF	0.708	1.328
IFNab	-0.756	0.287
IFNg	-0.775	-0.561
IFNg_GMCSF1	-0.666	0.229
Rv1432_day32	1.25	1.042
Rv1565c_day32	0.0	-1.703
secA2_input	-0.031	1.249
delta_Rv3594	0.909	-0.405
delta_Rv3717	0.893	-0.447
delta_Rv3811	0.721	-0.428
delta_Rv0954	0.699	-0.868
PonA1	0.278	-2.069
EccD1_KO	0.0	-0.257
EspI_KO	-0.419	-0.807
PE35_KO	-0.28	-0.166
PPE68_KO	0.099	0.0
glycerol2	1.1	0.792
lignocerate	0.956	0.737
oleate	0.719	1.311
phosphatidylcholine	0.634	1.045
acetate	0.459	0.359
glucAc	1.092	0.254
Rv0950ko	-0.292	-0.205
Rv1096ko	-0.048	-0.54
Rv3684ko	-0.373	-0.793
delta_otsA_trehalose	-1.372	-0.388