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 Rv3224A/-:

update plot	correlation	link to info on gene
Rv1987/-	(cc=0.5435)	info on Rv1987/-
Rv2587c/secD	(cc=0.5371)	info on Rv2587c/secD
Rv3224B/-	(cc=0.5299)	info on Rv3224B/-
Rv0590A/-	(cc=0.5244)	info on Rv0590A/-
Rv0312/-	(cc=0.5095)	info on Rv0312/-
Rv1738/-	(cc=0.507)	info on Rv1738/-
Rv0060/-	(cc=0.5002)	info on Rv0060/-
Rv0945/-	(cc=0.4933)	info on Rv0945/-
Rv0432/sodC	(cc=0.4855)	info on Rv0432/sodC
Rv2621c/-	(cc=0.4754)	info on Rv2621c/-

Correlation of Rv3224A/- with Rv0060/-

Normalized LFCs for Rv3224A/-:
(description and provenance of datasets)

	Rv3224A/-	Rv0060/-
Fe_supp_jason_reseq	2.797	0.391
low_pH_jason_reseq	-0.599	-1.134
NO_jason_reseq	-1.725	0.0
B6_jason_reseq	-2.259	0.0
MHCII_jason_reseq	-1.515	0.085
Isoniazid02	0.358	0.263
Rifampicin4	-1.013	0.712
Ethambutol3	-0.423	0.505
Meropenem3	-0.025	0.662
Vancomycin16	0.0	0.48
Rv2680_day32	2.963	-0.554
H37Rv_KO_MarP	0.035	0.35
hypoxia_3wks	-1.758	-0.606
hypoxia_6wks	-1.142	0.146
glycerol	-1.769	0.222
cholesterol	0.329	0.0
AJ	-1.153	0.131
Bibs02	-1.999	-1.123
Bibs02c	-1.238	0.629
BL6	1.287	0.53
BL6a	-0.366	0.595
BXD01	1.298	0.905
BXD010	-0.074	-0.543
BXD011	0.2	0.268
BXD03	1.017	0.52
BXD04	-1.167	-0.325
BXD05	-0.249	0.216
BXD06	-0.293	0.342
BXD07	0.983	0.0
BXD08	0.846	0.0
BXD09	-0.213	-0.173
CAST	-1.482	0.976
CCcont	2.065	1.498
DS01	0.932	-0.45
DS02	-2.757	1.235
DS04	0.84	0.312
DS0c	-2.203	-0.737
GP01	1.272	0.056
GP02	-0.91	-0.283
GP0c	1.505	0.942
NOD	-1.826	0.0
NZO	-2.728	0.6
PWK	-1.718	0.905
H37Rv_KO_CtpC	-2.222	0.977
H37Rv_KO_CtpD	2.993	0.989
H37Rv_KO_Rv1272	1.746	0.227
H37Rv_KO_SugABC	-1.083	0.877
H37Rv_KO_MbtN	-1.127	-0.633
Trans05	-0.649	-0.554
macrophage_unactivated	0.0	1.531
IL1	-4.108	-0.297
Rapamycin	-1.182	0.0
Tcell	1.147	1.352
GMCSF	0.457	-0.264
IFNab	2.038	0.0
IFNg	0.676	-0.551
IFNg_GMCSF1	-0.619	-0.314
Rv1432_day32	0.0	0.0
Rv1565c_day32	-1.403	-0.218
secA2_input	0.16	0.812
delta_Rv3594	3.02	0.961
delta_Rv3717	0.405	1.851
delta_Rv3811	3.359	1.335
delta_Rv0954	-1.742	0.0
PonA1	-1.714	-0.245
EccD1_KO	0.076	0.582
EspI_KO	-2.125	-0.787
PE35_KO	-0.353	-0.589
PPE68_KO	-0.387	-1.133
glycerol2	3.333	1.964
lignocerate	3.899	2.404
oleate	0.0	-0.688
phosphatidylcholine	3.332	1.909
acetate	4.833	2.128
glucAc	3.575	1.868
Rv0950ko	3.015	0.639
Rv1096ko	2.91	1.194
Rv3684ko	3.331	0.0
delta_otsA_trehalose	-2.329	0.366