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 Rv1696/recN:

update plot	correlation	link to info on gene
Rv2392/cysH	(cc=0.4219)	info on Rv2392/cysH
Rv2521/bcp	(cc=0.3942)	info on Rv2521/bcp
Rv1714/-	(cc=0.3923)	info on Rv1714/-
Rv3550/echA20	(cc=0.3823)	info on Rv3550/echA20
Rv1406/fmt	(cc=0.3797)	info on Rv1406/fmt
Rv2530A/vapB39	(cc=0.3746)	info on Rv2530A/vapB39
Rv1188/-	(cc=0.3721)	info on Rv1188/-
Rv0633c/-	(cc=0.3673)	info on Rv0633c/-
Rv0650/-	(cc=0.3607)	info on Rv0650/-
Rv1534/-	(cc=0.3585)	info on Rv1534/-

Correlation of Rv1696/recN with Rv2392/cysH

Normalized LFCs for Rv1696/recN:
(description and provenance of datasets)

	Rv1696/recN	Rv2392/cysH
Fe_supp_jason_reseq	-0.218	1.796
low_pH_jason_reseq	1.051	0.979
NO_jason_reseq	1.299	0.0
B6_jason_reseq	-1.184	0.0
MHCII_jason_reseq	-0.494	0.0
Isoniazid02	0.265	0.351
Rifampicin4	-0.076	-0.374
Ethambutol3	-0.14	0.0
Meropenem3	-0.103	0.151
Vancomycin16	0.0	-0.366
Rv2680_day32	0.816	0.0
H37Rv_KO_MarP	-0.512	-1.081
hypoxia_3wks	0.171	0.0
hypoxia_6wks	-0.495	0.0
glycerol	0.635	0.0
cholesterol	0.329	0.0
AJ	0.729	0.0
Bibs02	-1.274	0.0
Bibs02c	-1.458	0.0
BL6	-0.189	0.0
BL6a	-0.577	0.0
BXD01	0.036	0.0
BXD010	-0.194	0.0
BXD011	0.07	0.0
BXD03	-0.446	0.0
BXD04	0.1	0.0
BXD05	0.212	0.0
BXD06	-0.492	0.0
BXD07	0.283	0.0
BXD08	0.499	0.0
BXD09	0.186	0.0
CAST	-0.275	0.0
CCcont	0.531	0.0
DS01	0.792	0.0
DS02	0.06	0.0
DS04	-0.715	0.0
DS0c	0.979	0.0
GP01	0.808	0.0
GP02	-0.074	0.0
GP0c	0.204	0.0
NOD	-0.34	0.0
NZO	0.162	0.0
PWK	-0.114	0.0
H37Rv_KO_CtpC	-1.32	0.0
H37Rv_KO_CtpD	0.596	0.241
H37Rv_KO_Rv1272	0.761	0.0
H37Rv_KO_SugABC	0.63	0.0
H37Rv_KO_MbtN	-1.047	0.103
Trans05	0.267	0.0
macrophage_unactivated	-1.016	0.0
IL1	0.463	0.0
Rapamycin	0.479	0.0
Tcell	-0.137	0.0
GMCSF	0.412	0.0
IFNab	0.124	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	-0.698	0.0
Rv1432_day32	-1.027	0.0
Rv1565c_day32	1.308	0.0
secA2_input	0.631	-0.412
delta_Rv3594	0.985	0.211
delta_Rv3717	0.774	0.0
delta_Rv3811	0.129	0.0
delta_Rv0954	0.416	0.99
PonA1	0.84	0.979
EccD1_KO	0.102	0.378
EspI_KO	-0.473	-0.75
PE35_KO	-0.093	0.939
PPE68_KO	0.195	0.71
glycerol2	-0.601	0.0
lignocerate	0.278	0.0
oleate	-0.457	0.0
phosphatidylcholine	-0.181	0.0
acetate	1.041	0.0
glucAc	0.804	0.0
Rv0950ko	0.446	1.167
Rv1096ko	2.247	3.339
Rv3684ko	1.608	2.695
delta_otsA_trehalose	-1.369	0.133