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 Rv3172c/-:

update plot	correlation	link to info on gene
Rv3747/-	(cc=0.5001)	info on Rv3747/-
Rv2960c/-	(cc=0.4806)	info on Rv2960c/-
Rv3174/-	(cc=0.4735)	info on Rv3174/-
Rv0854/-	(cc=0.468)	info on Rv0854/-
Rv1290c/-	(cc=0.4656)	info on Rv1290c/-
Rv2958c/-	(cc=0.4401)	info on Rv2958c/-
Rv2809/-	(cc=0.435)	info on Rv2809/-
Rv2970A/-	(cc=0.4304)	info on Rv2970A/-
Rv3660c/-	(cc=0.4285)	info on Rv3660c/-
Rv1915/aceAa	(cc=0.4157)	info on Rv1915/aceAa

Correlation of Rv3172c/- with Rv2970A/-

Normalized LFCs for Rv3172c/-:
(description and provenance of datasets)

	Rv3172c/-	Rv2970A/-
Fe_supp_jason_reseq	0.672	1.023
low_pH_jason_reseq	-0.617	0.835
NO_jason_reseq	0.32	-0.572
B6_jason_reseq	0.496	0.598
MHCII_jason_reseq	0.991	-1.115
Isoniazid02	1.98	2.002
Rifampicin4	0.032	0.409
Ethambutol3	1.927	5.696
Meropenem3	-0.966	0.444
Vancomycin16	-0.485	0.846
Rv2680_day32	0.157	0.715
H37Rv_KO_MarP	0.08	0.968
hypoxia_3wks	-0.423	-0.778
hypoxia_6wks	-0.459	0.766
glycerol	-2.279	-0.389
cholesterol	-0.317	0.184
AJ	-0.983	-1.704
Bibs02	-0.061	-1.269
Bibs02c	0.055	0.303
BL6	0.471	3.312
BL6a	0.303	2.184
BXD01	0.25	2.485
BXD010	-0.433	1.936
BXD011	-0.087	2.424
BXD03	0.324	2.181
BXD04	-0.119	1.689
BXD05	0.438	3.209
BXD06	0.421	2.483
BXD07	-0.216	2.987
BXD08	0.445	1.885
BXD09	0.124	2.328
CAST	0.118	0.699
CCcont	0.662	2.221
DS01	0.106	0.527
DS02	-0.547	-0.866
DS04	-0.052	-1.196
DS0c	-0.338	-0.735
GP01	0.644	-1.621
GP02	-0.369	-1.116
GP0c	-0.089	-0.156
NOD	0.317	1.051
NZO	-0.387	-0.62
PWK	-0.629	0.118
H37Rv_KO_CtpC	0.293	0.293
H37Rv_KO_CtpD	0.472	0.051
H37Rv_KO_Rv1272	0.141	0.802
H37Rv_KO_SugABC	-0.43	-0.749
H37Rv_KO_MbtN	0.0	1.533
Trans05	0.858	0.0
macrophage_unactivated	-0.341	1.414
IL1	-0.635	1.706
Rapamycin	0.132	0.482
Tcell	0.378	0.577
GMCSF	0.0	0.304
IFNab	-0.354	1.684
IFNg	0.203	0.318
IFNg_GMCSF1	1.351	0.657
Rv1432_day32	-0.162	0.0
Rv1565c_day32	-0.153	-0.599
secA2_input	-0.042	2.779
delta_Rv3594	-0.493	-0.672
delta_Rv3717	-0.773	-0.248
delta_Rv3811	-0.375	-0.822
delta_Rv0954	-0.447	-2.417
PonA1	-0.532	0.0
EccD1_KO	-0.493	0.099
EspI_KO	-0.359	-0.89
PE35_KO	0.423	0.058
PPE68_KO	0.56	-0.032
glycerol2	0.5	0.835
lignocerate	1.199	2.012
oleate	-0.191	0.434
phosphatidylcholine	0.725	1.303
acetate	0.918	1.652
glucAc	0.955	1.092
Rv0950ko	-0.769	0.823
Rv1096ko	-0.341	-0.106
Rv3684ko	-0.521	-1.323
delta_otsA_trehalose	-0.074	-1.271