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 Rv3406/-:

update plot	correlation	link to info on gene
Rv2679/echA15	(cc=0.5782)	info on Rv2679/echA15
Rv0342/iniA	(cc=0.5703)	info on Rv0342/iniA
Rv3504/fadE26	(cc=0.5238)	info on Rv3504/fadE26
Rv3329/-	(cc=0.5224)	info on Rv3329/-
Rv0443/-	(cc=0.5187)	info on Rv0443/-
Rv3397c/phyA	(cc=0.5177)	info on Rv3397c/phyA
Rv3191c/-	(cc=0.505)	info on Rv3191c/-
Rv0399c/lpqK	(cc=0.5021)	info on Rv0399c/lpqK
Rv0968/-	(cc=0.4967)	info on Rv0968/-
Rv0104/-	(cc=0.4936)	info on Rv0104/-

Correlation of Rv3406/- with Rv0104/-

Normalized LFCs for Rv3406/-:
(description and provenance of datasets)

	Rv3406/-	Rv0104/-
Fe_supp_jason_reseq	-0.343	-0.035
low_pH_jason_reseq	-0.477	-0.174
NO_jason_reseq	-0.347	-0.312
B6_jason_reseq	-0.298	-0.115
MHCII_jason_reseq	0.298	0.219
Isoniazid02	-1.986	-1.328
Rifampicin4	0.368	0.493
Ethambutol3	-1.893	-0.627
Meropenem3	-0.167	-0.302
Vancomycin16	-0.748	-0.432
Rv2680_day32	-0.062	-0.48
H37Rv_KO_MarP	0.524	0.381
hypoxia_3wks	-0.032	-0.108
hypoxia_6wks	-0.386	-0.436
glycerol	0.023	0.14
cholesterol	-0.246	-0.071
AJ	0.531	-0.341
Bibs02	0.201	0.177
Bibs02c	-0.662	0.062
BL6	1.034	0.595
BL6a	0.145	0.255
BXD01	-0.008	-0.089
BXD010	0.811	0.686
BXD011	0.153	0.15
BXD03	-0.158	0.024
BXD04	0.425	0.079
BXD05	0.565	0.502
BXD06	0.274	0.0
BXD07	0.336	0.119
BXD08	0.023	-0.196
BXD09	0.494	0.253
CAST	0.46	-0.23
CCcont	0.043	0.3
DS01	0.31	-0.056
DS02	-0.05	0.09
DS04	0.077	0.25
DS0c	-0.239	0.013
GP01	0.288	1.17
GP02	1.221	0.736
GP0c	-0.528	0.733
NOD	0.809	-0.21
NZO	-0.194	0.012
PWK	0.512	0.07
H37Rv_KO_CtpC	-0.067	0.53
H37Rv_KO_CtpD	0.795	0.483
H37Rv_KO_Rv1272	-0.911	-0.416
H37Rv_KO_SugABC	0.155	1.248
H37Rv_KO_MbtN	-0.211	0.358
Trans05	-0.565	0.331
macrophage_unactivated	-0.331	-0.041
IL1	0.039	-0.433
Rapamycin	-0.04	0.058
Tcell	0.124	0.14
GMCSF	0.195	0.016
IFNab	-0.218	-0.193
IFNg	0.449	-0.067
IFNg_GMCSF1	0.251	-0.223
Rv1432_day32	0.252	0.269
Rv1565c_day32	-0.24	-0.014
secA2_input	-0.016	-0.559
delta_Rv3594	-0.465	0.567
delta_Rv3717	-0.262	0.488
delta_Rv3811	-0.149	0.72
delta_Rv0954	0.419	0.842
PonA1	0.259	1.024
EccD1_KO	0.691	-0.086
EspI_KO	0.046	-0.519
PE35_KO	-0.047	-0.111
PPE68_KO	-0.211	-0.291
glycerol2	0.553	0.476
lignocerate	0.225	0.939
oleate	0.527	0.109
phosphatidylcholine	0.5	0.462
acetate	0.219	0.994
glucAc	0.06	0.805
Rv0950ko	0.573	0.591
Rv1096ko	0.694	0.905
Rv3684ko	0.151	0.92
delta_otsA_trehalose	1.329	0.359