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 Rv3148/nuoD

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

	Rv0235c/-	Rv3148/nuoD
Fe_supp_jason_reseq	-0.783	-0.747
low_pH_jason_reseq	-0.204	-1.603
NO_jason_reseq	0.0	0.0
B6_jason_reseq	-0.687	-1.364
MHCII_jason_reseq	-0.63	-1.656
Isoniazid02	0.164	-0.167
Rifampicin4	0.0	-0.536
Ethambutol3	0.035	-0.461
Meropenem3	0.035	0.625
Vancomycin16	0.0	-0.305
Rv2680_day32	0.105	-0.344
H37Rv_KO_MarP	0.155	-0.531
hypoxia_3wks	0.191	0.51
hypoxia_6wks	-0.443	-0.372
glycerol	0.075	-1.121
cholesterol	-0.055	-0.091
AJ	0.086	-0.471
Bibs02	-1.13	-0.666
Bibs02c	0.039	-0.762
BL6	1.27	1.692
BL6a	1.072	2.431
BXD01	1.126	2.091
BXD010	0.904	2.004
BXD011	0.508	2.011
BXD03	1.42	2.586
BXD04	1.098	2.913
BXD05	0.447	1.652
BXD06	0.863	2.414
BXD07	1.406	2.259
BXD08	0.874	1.927
BXD09	0.578	2.845
CAST	0.205	1.366
CCcont	1.15	2.093
DS01	0.044	0.636
DS02	-0.082	-0.441
DS04	0.394	-0.122
DS0c	-0.041	1.996
GP01	1.319	0.477
GP02	2.076	1.166
GP0c	0.788	1.596
NOD	0.866	-0.818
NZO	0.212	0.538
PWK	0.571	0.227
H37Rv_KO_CtpC	1.221	0.654
H37Rv_KO_CtpD	-0.661	1.713
H37Rv_KO_Rv1272	0.451	2.611
H37Rv_KO_SugABC	1.891	1.666
H37Rv_KO_MbtN	0.462	2.158
Trans05	1.231	2.349
macrophage_unactivated	0.805	-0.095
IL1	0.0	-0.658
Rapamycin	-0.592	-0.184
Tcell	0.209	0.873
GMCSF	0.708	0.576
IFNab	-0.756	0.883
IFNg	-0.775	-0.243
IFNg_GMCSF1	-0.666	-0.698
Rv1432_day32	1.25	-0.383
Rv1565c_day32	0.0	0.058
secA2_input	-0.031	-0.081
delta_Rv3594	0.909	0.733
delta_Rv3717	0.893	0.35
delta_Rv3811	0.721	0.665
delta_Rv0954	0.699	0.404
PonA1	0.278	0.553
EccD1_KO	0.0	-0.97
EspI_KO	-0.419	1.241
PE35_KO	-0.28	0.373
PPE68_KO	0.099	0.41
glycerol2	1.1	2.114
lignocerate	0.956	0.365
oleate	0.719	1.642
phosphatidylcholine	0.634	0.87
acetate	0.459	0.499
glucAc	1.092	2.885
Rv0950ko	-0.292	-0.362
Rv1096ko	-0.048	-0.492
Rv3684ko	-0.373	-0.534
delta_otsA_trehalose	-1.372	0.528