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 Rv1675c/cmr:

update plot	correlation	link to info on gene
Rv0373c/-	(cc=0.5903)	info on Rv0373c/-
Rv0338c/-	(cc=0.5732)	info on Rv0338c/-
Rv0063/-	(cc=0.5603)	info on Rv0063/-
Rv0320/-	(cc=0.5585)	info on Rv0320/-
Rv2268c/cyp128	(cc=0.4947)	info on Rv2268c/cyp128
Rv2431c/PE25	(cc=0.481)	info on Rv2431c/PE25
Rv3624c/hpt	(cc=0.4743)	info on Rv3624c/hpt
Rv0625c/-	(cc=0.4709)	info on Rv0625c/-
Rv1701/-	(cc=0.4669)	info on Rv1701/-
Rv3844/-	(cc=0.4656)	info on Rv3844/-

Correlation of Rv1675c/cmr with Rv0338c/-

Normalized LFCs for Rv1675c/cmr:
(description and provenance of datasets)

	Rv1675c/cmr	Rv0338c/-
Fe_supp_jason_reseq	-0.17	0.0
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.179	0.0
B6_jason_reseq	-0.162	0.0
MHCII_jason_reseq	1.183	0.0
Isoniazid02	-0.63	0.0
Rifampicin4	-1.124	0.0
Ethambutol3	-0.786	0.0
Meropenem3	-0.394	0.0
Vancomycin16	-0.613	0.0
Rv2680_day32	-0.08	0.0
H37Rv_KO_MarP	0.109	0.0
hypoxia_3wks	-0.805	0.0
hypoxia_6wks	-0.464	0.0
glycerol	1.179	0.385
cholesterol	5.239	3.545
AJ	0.371	0.0
Bibs02	0.306	0.0
Bibs02c	1.015	0.0
BL6	0.303	0.0
BL6a	0.317	0.0
BXD01	-1.107	0.0
BXD010	-0.084	0.0
BXD011	0.143	0.0
BXD03	0.357	0.0
BXD04	-1.13	0.0
BXD05	0.645	0.0
BXD06	0.693	0.0
BXD07	0.232	0.0
BXD08	-0.671	0.0
BXD09	0.012	0.0
CAST	0.507	0.0
CCcont	-0.82	0.0
DS01	0.145	0.0
DS02	0.153	0.0
DS04	0.839	0.0
DS0c	0.244	0.0
GP01	-0.23	0.0
GP02	-1.06	0.0
GP0c	-0.333	0.0
NOD	-0.021	0.0
NZO	0.649	0.0
PWK	-0.054	0.0
H37Rv_KO_CtpC	0.272	0.0
H37Rv_KO_CtpD	0.99	0.0
H37Rv_KO_Rv1272	-0.554	0.0
H37Rv_KO_SugABC	-1.147	0.0
H37Rv_KO_MbtN	-1.313	0.0
Trans05	0.934	0.0
macrophage_unactivated	-0.944	0.0
IL1	-0.222	0.0
Rapamycin	-0.724	0.0
Tcell	-1.274	0.0
GMCSF	0.789	0.0
IFNab	0.094	0.0
IFNg	-0.23	0.0
IFNg_GMCSF1	0.097	0.0
Rv1432_day32	-2.941	0.0
Rv1565c_day32	0.619	0.0
secA2_input	-0.739	0.847
delta_Rv3594	0.058	0.0
delta_Rv3717	-0.292	0.0
delta_Rv3811	0.909	0.0
delta_Rv0954	-1.012	0.0
PonA1	0.705	0.0
EccD1_KO	-0.184	0.0
EspI_KO	-1.728	0.0
PE35_KO	-0.697	0.0
PPE68_KO	-1.142	0.0
glycerol2	-2.609	0.0
lignocerate	-0.756	0.0
oleate	-2.64	0.0
phosphatidylcholine	-1.852	0.0
acetate	0.06	0.0
glucAc	-0.242	0.0
Rv0950ko	0.199	0.0
Rv1096ko	-0.721	0.0
Rv3684ko	0.111	0.0
delta_otsA_trehalose	-0.987	0.133