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 Rv2947c/pks15:

update plot	correlation	link to info on gene
Rv1947/-	(cc=0.5793)	info on Rv1947/-
Rv3145/nuoA	(cc=0.5518)	info on Rv3145/nuoA
Rv2352c/PPE38	(cc=0.5506)	info on Rv2352c/PPE38
Rv2345/-	(cc=0.5434)	info on Rv2345/-
Rv3397c/phyA	(cc=0.5279)	info on Rv3397c/phyA
Rv3125c/PPE49	(cc=0.5199)	info on Rv3125c/PPE49
Rv1169c/lipX	(cc=0.5197)	info on Rv1169c/lipX
Rv3116/moeB2	(cc=0.517)	info on Rv3116/moeB2
Rv1167c/-	(cc=0.5124)	info on Rv1167c/-
Rv3161c/-	(cc=0.5086)	info on Rv3161c/-

Correlation of Rv2947c/pks15 with Rv1167c/-

Normalized LFCs for Rv2947c/pks15:
(description and provenance of datasets)

	Rv2947c/pks15	Rv1167c/-
Fe_supp_jason_reseq	-0.232	-1.156
low_pH_jason_reseq	-0.918	0.448
NO_jason_reseq	-0.263	1.88
B6_jason_reseq	-0.674	-2.005
MHCII_jason_reseq	-0.437	-2.389
Isoniazid02	-1.55	-2.878
Rifampicin4	0.222	-1.338
Ethambutol3	-0.967	-1.589
Meropenem3	-0.809	-1.935
Vancomycin16	-0.634	-2.921
Rv2680_day32	-0.55	-1.565
H37Rv_KO_MarP	-0.322	0.969
hypoxia_3wks	1.009	-0.159
hypoxia_6wks	0.514	-0.213
glycerol	0.14	0.088
cholesterol	-0.031	-1.082
AJ	-0.44	-1.256
Bibs02	0.465	-1.06
Bibs02c	0.103	-0.708
BL6	0.852	0.775
BL6a	0.267	0.326
BXD01	0.546	0.869
BXD010	0.287	1.656
BXD011	0.25	0.865
BXD03	0.48	0.642
BXD04	0.708	0.882
BXD05	0.351	0.913
BXD06	0.494	0.495
BXD07	-0.054	1.559
BXD08	0.539	1.349
BXD09	-0.061	0.626
CAST	-0.14	0.148
CCcont	0.293	1.736
DS01	0.192	-0.873
DS02	-0.038	-1.26
DS04	0.842	-0.228
DS0c	0.126	0.047
GP01	0.584	0.8
GP02	0.151	-0.835
GP0c	-0.006	-0.089
NOD	-0.293	-1.578
NZO	-0.368	-0.614
PWK	0.342	-1.137
H37Rv_KO_CtpC	1.048	2.015
H37Rv_KO_CtpD	-0.017	1.663
H37Rv_KO_Rv1272	0.966	0.455
H37Rv_KO_SugABC	0.609	-0.938
H37Rv_KO_MbtN	0.417	0.299
Trans05	0.552	0.443
macrophage_unactivated	0.505	0.249
IL1	0.113	0.866
Rapamycin	-0.709	0.559
Tcell	0.411	1.636
GMCSF	0.238	0.481
IFNab	0.115	0.048
IFNg	-0.075	0.673
IFNg_GMCSF1	0.886	0.751
Rv1432_day32	-0.512	-1.949
Rv1565c_day32	-1.281	-0.499
secA2_input	-0.013	0.266
delta_Rv3594	0.488	0.693
delta_Rv3717	0.313	-0.021
delta_Rv3811	0.474	-0.617
delta_Rv0954	-0.217	-0.69
PonA1	0.287	0.0
EccD1_KO	0.289	0.661
EspI_KO	0.251	-0.722
PE35_KO	0.846	0.28
PPE68_KO	1.008	0.55
glycerol2	0.238	-0.319
lignocerate	-0.158	-0.196
oleate	0.241	-0.906
phosphatidylcholine	0.262	0.032
acetate	-0.545	0.17
glucAc	-0.258	0.255
Rv0950ko	-0.069	-1.357
Rv1096ko	0.054	-1.357
Rv3684ko	-0.766	-1.153
delta_otsA_trehalose	0.244	-0.245