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 Rv3792/aftA:

update plot	correlation	link to info on gene
Rv3588c/canB	(cc=0.5238)	info on Rv3588c/canB
Rv2256c/-	(cc=0.5019)	info on Rv2256c/-
Rv3035/-	(cc=0.498)	info on Rv3035/-
Rv2067c/-	(cc=0.4972)	info on Rv2067c/-
Rv3410c/guaB3	(cc=0.4667)	info on Rv3410c/guaB3
Rv1917c/PPE34	(cc=0.4624)	info on Rv1917c/PPE34
Rv2400c/subI	(cc=0.4583)	info on Rv2400c/subI
Rv1521/fadD25	(cc=0.4538)	info on Rv1521/fadD25
Rv2399c/cysT	(cc=0.4527)	info on Rv2399c/cysT
Rv1509/-	(cc=0.4502)	info on Rv1509/-

Correlation of Rv3792/aftA with Rv2400c/subI

Normalized LFCs for Rv3792/aftA:
(description and provenance of datasets)

	Rv3792/aftA	Rv2400c/subI
Fe_supp_jason_reseq	0.0	0.766
low_pH_jason_reseq	-0.44	0.0
NO_jason_reseq	-0.69	0.0
B6_jason_reseq	0.558	0.0
MHCII_jason_reseq	-0.123	0.0
Isoniazid02	0.0	-1.072
Rifampicin4	0.0	-1.681
Ethambutol3	0.0	-0.755
Meropenem3	0.0	-1.033
Vancomycin16	0.0	-1.647
Rv2680_day32	0.131	0.0
H37Rv_KO_MarP	-0.34	-1.307
hypoxia_3wks	-0.55	0.0
hypoxia_6wks	0.503	0.0
glycerol	0.0	0.0
cholesterol	-0.145	0.0
AJ	0.405	0.0
Bibs02	-0.183	0.0
Bibs02c	-0.209	0.0
BL6	0.964	0.0
BL6a	0.0	0.0
BXD01	-0.13	0.0
BXD010	0.583	0.0
BXD011	-0.127	0.0
BXD03	0.0	0.0
BXD04	-0.124	0.0
BXD05	-0.135	0.0
BXD06	-0.133	0.0
BXD07	0.242	0.0
BXD08	0.232	0.0
BXD09	-0.14	0.0
CAST	0.402	0.0
CCcont	0.136	0.285
DS01	-0.236	0.0
DS02	-0.217	0.0
DS04	-0.194	0.0
DS0c	-0.217	0.0
GP01	0.449	0.0
GP02	1.986	0.0
GP0c	0.51	0.0
NOD	0.205	0.0
NZO	0.0	0.0
PWK	0.179	0.0
H37Rv_KO_CtpC	0.0	0.0
H37Rv_KO_CtpD	1.237	0.127
H37Rv_KO_Rv1272	-0.141	0.0
H37Rv_KO_SugABC	-0.099	0.0
H37Rv_KO_MbtN	0.53	0.0
Trans05	0.329	0.0
macrophage_unactivated	0.363	0.0
IL1	-0.374	0.0
Rapamycin	0.0	0.0
Tcell	-0.411	0.0
GMCSF	-0.333	0.0
IFNab	0.0	0.0
IFNg	-0.337	0.0
IFNg_GMCSF1	-0.396	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	-0.269	0.218
secA2_input	-0.128	-2.069
delta_Rv3594	-0.164	0.211
delta_Rv3717	-0.135	0.0
delta_Rv3811	-0.518	0.0
delta_Rv0954	0.129	1.383
PonA1	-0.256	0.884
EccD1_KO	-0.378	-5.825
EspI_KO	-0.687	-6.0
PE35_KO	0.312	2.333
PPE68_KO	-0.368	-0.595
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	0.143	0.0
Rv0950ko	-0.844	-3.585
Rv1096ko	-1.517	-3.673
Rv3684ko	-1.647	-3.799
delta_otsA_trehalose	0.0	1.223