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 Rv1436/gap:

update plot	correlation	link to info on gene
Rv2130c/mshC	(cc=0.8763)	info on Rv2130c/mshC
Rv3603c/-	(cc=0.8488)	info on Rv3603c/-
Rv1002c/-	(cc=0.8007)	info on Rv1002c/-
Rv1208/gpgS	(cc=0.7808)	info on Rv1208/gpgS
Rv3601c/panD	(cc=0.7527)	info on Rv3601c/panD
Rv0411c/glnH	(cc=0.7423)	info on Rv0411c/glnH
Rv1437/pgk	(cc=0.7369)	info on Rv1437/pgk
Rv2844/-	(cc=0.7192)	info on Rv2844/-
Rv2847c/cysG	(cc=0.669)	info on Rv2847c/cysG
Rv2470/glbO	(cc=0.6659)	info on Rv2470/glbO

Correlation of Rv1436/gap with Rv2844/-

Normalized LFCs for Rv1436/gap:
(description and provenance of datasets)

	Rv1436/gap	Rv2844/-
Fe_supp_jason_reseq	0.218	0.0
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	0.0	-0.383
Rifampicin4	0.0	-0.712
Ethambutol3	0.0	-0.153
Meropenem3	0.0	-0.151
Vancomycin16	0.0	-0.698
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-1.307	-3.233
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	1.082
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.194
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	0.0	0.0
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.0
H37Rv_KO_MbtN	0.0	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	-0.7	0.388
delta_Rv3594	0.0	0.493
delta_Rv3717	0.0	-0.331
delta_Rv3811	0.0	-0.187
delta_Rv0954	0.34	-0.34
PonA1	0.0	1.009
EccD1_KO	0.0	0.352
EspI_KO	0.0	-0.687
PE35_KO	1.978	4.728
PPE68_KO	2.169	4.3
glycerol2	-0.369	0.0
lignocerate	-0.32	0.168
oleate	-0.373	0.0
phosphatidylcholine	-0.368	0.0
acetate	-0.437	0.0
glucAc	-0.272	0.0
Rv0950ko	0.347	-3.015
Rv1096ko	-0.793	-1.873
Rv3684ko	0.727	-1.359
delta_otsA_trehalose	0.0	0.893