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 Rv2392/cysH:

update plot	correlation	link to info on gene
Rv2391/sirA	(cc=0.7309)	info on Rv2391/sirA
Rv1406/fmt	(cc=0.6574)	info on Rv1406/fmt
Rv2445c/ndkA	(cc=0.6185)	info on Rv2445c/ndkA
Rv0287/esxG	(cc=0.5982)	info on Rv0287/esxG
Rv0633c/-	(cc=0.5297)	info on Rv0633c/-
Rv1348/irtA	(cc=0.5216)	info on Rv1348/irtA
Rv3601c/panD	(cc=0.5164)	info on Rv3601c/panD
Rv3139/fadE24	(cc=0.5049)	info on Rv3139/fadE24
Rv3276c/purK	(cc=0.4954)	info on Rv3276c/purK
Rv0410c/pknG	(cc=0.4897)	info on Rv0410c/pknG

Correlation of Rv2392/cysH with Rv2391/sirA

Normalized LFCs for Rv2392/cysH:
(description and provenance of datasets)

	Rv2392/cysH	Rv2391/sirA
Fe_supp_jason_reseq	1.796	0.766
low_pH_jason_reseq	0.979	0.979
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	0.351	2.673
Rifampicin4	-0.374	-0.601
Ethambutol3	0.0	-0.27
Meropenem3	0.151	-0.128
Vancomycin16	-0.366	-0.589
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-1.081	-1.081
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.0	0.0
cholesterol	0.0	0.0
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	0.0	0.0
BL6a	0.0	0.0
BXD01	0.0	0.0
BXD010	0.0	0.0
BXD011	0.0	0.0
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.0	0.0
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	0.0	0.149
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.0
DS0c	0.0	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.0	0.0
H37Rv_KO_CtpD	0.241	0.348
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.0
H37Rv_KO_MbtN	0.103	0.103
Trans05	0.0	0.0
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-0.412	-0.167
delta_Rv3594	0.211	-0.211
delta_Rv3717	0.0	-0.174
delta_Rv3811	0.0	-0.205
delta_Rv0954	0.99	1.018
PonA1	0.979	0.402
EccD1_KO	0.378	-0.352
EspI_KO	-0.75	-0.633
PE35_KO	0.939	2.088
PPE68_KO	0.71	1.411
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.0
glucAc	0.0	0.0
Rv0950ko	1.167	0.609
Rv1096ko	3.339	1.463
Rv3684ko	2.695	1.916
delta_otsA_trehalose	0.133	0.254