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 Rv2591/PE_PGRS44:

update plot	correlation	link to info on gene
Rv1191/-	(cc=0.4738)	info on Rv1191/-
Rv1214c/PE14	(cc=0.4558)	info on Rv1214c/PE14
Rv3446c/-	(cc=0.4558)	info on Rv3446c/-
Rv0833/PE_PGRS13	(cc=0.43)	info on Rv0833/PE_PGRS13
Rv1767/-	(cc=0.4242)	info on Rv1767/-
Rv2183c/-	(cc=0.4208)	info on Rv2183c/-
Rv3555c/-	(cc=0.4069)	info on Rv3555c/-
Rv2870c/dxr	(cc=0.4011)	info on Rv2870c/dxr
Rv3713/cobQ2	(cc=0.4001)	info on Rv3713/cobQ2
Rv3344c/PE_PGRS49	(cc=0.3987)	info on Rv3344c/PE_PGRS49

Correlation of Rv2591/PE_PGRS44 with Rv3713/cobQ2

Normalized LFCs for Rv2591/PE_PGRS44:
(description and provenance of datasets)

	Rv2591/PE_PGRS44	Rv3713/cobQ2
Fe_supp_jason_reseq	-1.695	-1.07
low_pH_jason_reseq	1.337	0.656
NO_jason_reseq	0.562	0.0
B6_jason_reseq	-0.712	-0.752
MHCII_jason_reseq	0.148	-0.663
Isoniazid02	0.017	-0.221
Rifampicin4	0.983	0.872
Ethambutol3	0.687	0.0
Meropenem3	1.72	2.19
Vancomycin16	0.676	0.698
Rv2680_day32	-0.08	0.0
H37Rv_KO_MarP	0.154	-0.371
hypoxia_3wks	0.686	0.0
hypoxia_6wks	-0.43	0.0
glycerol	0.769	0.0
cholesterol	0.145	0.0
AJ	0.541	0.0
Bibs02	0.813	0.0
Bibs02c	0.453	0.0
BL6	0.112	0.0
BL6a	0.769	0.0
BXD01	0.525	0.0
BXD010	0.013	0.0
BXD011	0.485	0.0
BXD03	0.082	0.0
BXD04	1.411	0.0
BXD05	0.38	0.0
BXD06	0.207	0.0
BXD07	0.606	0.0
BXD08	0.778	0.0
BXD09	0.462	0.0
CAST	-0.661	0.0
CCcont	0.41	0.0
DS01	0.074	0.0
DS02	0.11	0.0
DS04	-1.14	0.0
DS0c	-0.713	0.0
GP01	1.257	0.0
GP02	0.952	0.0
GP0c	0.753	0.0
NOD	-0.047	0.0
NZO	1.081	0.0
PWK	0.357	0.0
H37Rv_KO_CtpC	0.222	0.0
H37Rv_KO_CtpD	0.778	1.315
H37Rv_KO_Rv1272	0.1	0.0
H37Rv_KO_SugABC	0.248	0.0
H37Rv_KO_MbtN	0.603	0.0
Trans05	-0.114	0.0
macrophage_unactivated	0.205	0.0
IL1	-0.703	0.0
Rapamycin	0.058	0.0
Tcell	-0.287	0.0
GMCSF	-0.153	0.0
IFNab	-0.617	0.0
IFNg	0.126	0.0
IFNg_GMCSF1	-0.606	0.0
Rv1432_day32	0.484	0.0
Rv1565c_day32	0.698	0.0
secA2_input	-0.75	0.504
delta_Rv3594	0.835	0.0
delta_Rv3717	1.13	0.174
delta_Rv3811	0.394	0.0
delta_Rv0954	-0.109	0.0
PonA1	0.053	0.0
EccD1_KO	0.658	-0.454
EspI_KO	1.309	-0.394
PE35_KO	-0.067	0.368
PPE68_KO	-0.182	-0.442
glycerol2	0.314	0.0
lignocerate	-0.029	0.0
oleate	0.583	0.0
phosphatidylcholine	0.567	0.0
acetate	0.254	0.0
glucAc	-0.465	0.0
Rv0950ko	0.51	0.0
Rv1096ko	0.48	0.0
Rv3684ko	1.601	0.0
delta_otsA_trehalose	-0.591	0.133