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 Rv2775/-:

update plot	correlation	link to info on gene
Rv1498c/-	(cc=0.6072)	info on Rv1498c/-
Rv2452c/-	(cc=0.5921)	info on Rv2452c/-
Rv2957/-	(cc=0.5567)	info on Rv2957/-
Rv1500/-	(cc=0.549)	info on Rv1500/-
Rv1583c/-	(cc=0.5471)	info on Rv1583c/-
Rv2267c/-	(cc=0.5409)	info on Rv2267c/-
Rv2881c/cdsA	(cc=0.5309)	info on Rv2881c/cdsA
Rv3628/ppa	(cc=0.5264)	info on Rv3628/ppa
Rv3429/PPE59	(cc=0.524)	info on Rv3429/PPE59
Rv1116/-	(cc=0.5156)	info on Rv1116/-

Correlation of Rv2775/- with Rv1498c/-

Normalized LFCs for Rv2775/-:
(description and provenance of datasets)

	Rv2775/-	Rv1498c/-
Fe_supp_jason_reseq	0.466	1.557
low_pH_jason_reseq	-0.037	0.499
NO_jason_reseq	-0.977	0.339
B6_jason_reseq	0.469	-0.235
MHCII_jason_reseq	-0.364	-0.081
Isoniazid02	-0.389	-1.26
Rifampicin4	-0.038	0.23
Ethambutol3	-0.276	-1.16
Meropenem3	-1.548	-1.318
Vancomycin16	-0.127	-0.806
Rv2680_day32	-0.205	0.016
H37Rv_KO_MarP	-0.666	-0.631
hypoxia_3wks	-0.817	0.443
hypoxia_6wks	0.058	0.092
glycerol	-1.814	-0.064
cholesterol	-1.544	0.441
AJ	0.474	0.402
Bibs02	-1.113	0.525
Bibs02c	-0.1	-0.189
BL6	0.246	0.969
BL6a	0.595	0.65
BXD01	0.083	0.548
BXD010	1.009	1.26
BXD011	0.952	1.351
BXD03	0.569	0.869
BXD04	0.432	0.713
BXD05	2.161	1.417
BXD06	1.25	0.962
BXD07	0.675	0.97
BXD08	0.499	0.654
BXD09	0.951	0.855
CAST	0.592	-0.35
CCcont	0.59	0.82
DS01	0.994	0.517
DS02	-0.378	-0.391
DS04	0.037	0.817
DS0c	-0.192	0.434
GP01	1.913	0.704
GP02	0.55	0.51
GP0c	1.296	0.225
NOD	1.394	1.538
NZO	0.162	0.548
PWK	1.047	0.644
H37Rv_KO_CtpC	0.599	1.414
H37Rv_KO_CtpD	1.142	0.01
H37Rv_KO_Rv1272	1.787	0.942
H37Rv_KO_SugABC	1.287	1.369
H37Rv_KO_MbtN	0.538	0.905
Trans05	1.467	1.564
macrophage_unactivated	0.524	0.404
IL1	-0.35	0.08
Rapamycin	0.964	0.015
Tcell	-0.775	0.384
GMCSF	0.525	-0.071
IFNab	0.747	0.082
IFNg	0.083	0.633
IFNg_GMCSF1	0.019	0.54
Rv1432_day32	0.113	0.282
Rv1565c_day32	0.199	0.646
secA2_input	0.172	-0.233
delta_Rv3594	-0.812	-0.205
delta_Rv3717	-1.117	-0.238
delta_Rv3811	-1.056	-0.691
delta_Rv0954	-1.181	-0.702
PonA1	-2.209	-0.268
EccD1_KO	0.506	0.865
EspI_KO	1.269	0.85
PE35_KO	1.502	1.397
PPE68_KO	1.574	1.667
glycerol2	0.0	0.252
lignocerate	0.935	0.818
oleate	-1.208	0.109
phosphatidylcholine	0.629	0.374
acetate	0.469	0.332
glucAc	0.563	0.76
Rv0950ko	0.389	0.241
Rv1096ko	0.178	-0.908
Rv3684ko	-0.098	-0.301
delta_otsA_trehalose	-0.085	-1.361