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 Rv1002c/-:

update plot	correlation	link to info on gene
Rv2130c/mshC	(cc=0.8843)	info on Rv2130c/mshC
Rv1436/gap	(cc=0.8007)	info on Rv1436/gap
Rv2507/-	(cc=0.7836)	info on Rv2507/-
Rv0127/mak	(cc=0.7438)	info on Rv0127/mak
Rv1208/gpgS	(cc=0.737)	info on Rv1208/gpgS
Rv0411c/glnH	(cc=0.7193)	info on Rv0411c/glnH
Rv3601c/panD	(cc=0.7148)	info on Rv3601c/panD
Rv3212/-	(cc=0.7048)	info on Rv3212/-
Rv0410c/pknG	(cc=0.6534)	info on Rv0410c/pknG
Rv0412c/-	(cc=0.6477)	info on Rv0412c/-

Correlation of Rv1002c/- with Rv0410c/pknG

Normalized LFCs for Rv1002c/-:
(description and provenance of datasets)

	Rv1002c/-	Rv0410c/pknG
Fe_supp_jason_reseq	-0.415	0.598
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.302	0.0
B6_jason_reseq	-0.292	0.0
MHCII_jason_reseq	-0.257	0.0
Isoniazid02	0.0	-0.201
Rifampicin4	0.0	-0.374
Ethambutol3	0.0	-0.168
Meropenem3	0.0	-0.165
Vancomycin16	0.0	-0.366
Rv2680_day32	0.0	-0.459
H37Rv_KO_MarP	-1.696	-3.779
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	0.127
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	1.157
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.0
DS0c	0.0	0.217
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	0.162
H37Rv_KO_CtpD	0.0	0.241
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.0
H37Rv_KO_MbtN	0.0	0.283
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	-0.348	0.167
delta_Rv3594	0.0	0.0
delta_Rv3717	0.174	0.0
delta_Rv3811	0.564	0.0
delta_Rv0954	0.627	0.876
PonA1	0.0	4.022
EccD1_KO	0.0	-0.865
EspI_KO	0.516	-1.275
PE35_KO	1.8	2.774
PPE68_KO	2.358	2.627
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.229
glucAc	0.0	0.0
Rv0950ko	-0.971	-0.739
Rv1096ko	-0.302	0.389
Rv3684ko	2.414	1.611
delta_otsA_trehalose	0.0	-0.133