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 Rv3165c/-:

update plot	correlation	link to info on gene
Rv2740/ephG	(cc=0.4995)	info on Rv2740/ephG
Rv0769/-	(cc=0.4668)	info on Rv0769/-
Rv0499/-	(cc=0.4548)	info on Rv0499/-
Rv1499/-	(cc=0.4524)	info on Rv1499/-
Rv2308/-	(cc=0.4365)	info on Rv2308/-
Rv2060/-	(cc=0.4245)	info on Rv2060/-
Rv1219c/-	(cc=0.4109)	info on Rv1219c/-
Rv3553/-	(cc=0.4092)	info on Rv3553/-
Rv1082/mca	(cc=0.4085)	info on Rv1082/mca
Rv2437/-	(cc=0.4063)	info on Rv2437/-

Correlation of Rv3165c/- with Rv0499/-

Normalized LFCs for Rv3165c/-:
(description and provenance of datasets)

	Rv3165c/-	Rv0499/-
Fe_supp_jason_reseq	1.427	0.152
low_pH_jason_reseq	0.151	0.209
NO_jason_reseq	-1.394	0.06
B6_jason_reseq	0.333	-0.542
MHCII_jason_reseq	0.308	-1.733
Isoniazid02	-0.295	0.319
Rifampicin4	-0.309	0.609
Ethambutol3	-0.652	0.331
Meropenem3	0.024	0.152
Vancomycin16	0.027	0.435
Rv2680_day32	2.941	-0.46
H37Rv_KO_MarP	0.684	1.35
hypoxia_3wks	-0.327	0.032
hypoxia_6wks	-0.503	0.451
glycerol	0.718	0.579
cholesterol	-0.506	-0.994
AJ	0.128	0.449
Bibs02	-0.603	-0.832
Bibs02c	-1.291	-0.746
BL6	-0.342	0.127
BL6a	0.161	-0.362
BXD01	0.173	-0.747
BXD010	1.189	-0.168
BXD011	0.478	0.816
BXD03	0.706	-0.135
BXD04	0.913	-0.108
BXD05	-0.249	1.044
BXD06	0.829	0.161
BXD07	0.687	0.255
BXD08	0.143	-0.053
BXD09	0.486	0.534
CAST	0.305	-0.105
CCcont	0.661	0.453
DS01	-0.32	-2.19
DS02	-2.757	-0.775
DS04	-1.577	-1.249
DS0c	-0.715	-0.896
GP01	-0.715	0.998
GP02	-1.448	-0.608
GP0c	-0.98	0.499
NOD	-0.199	0.465
NZO	0.564	-0.273
PWK	0.159	0.406
H37Rv_KO_CtpC	-0.567	-0.753
H37Rv_KO_CtpD	1.921	0.014
H37Rv_KO_Rv1272	-0.082	-0.998
H37Rv_KO_SugABC	-0.562	-1.522
H37Rv_KO_MbtN	0.877	0.816
Trans05	1.323	-0.319
macrophage_unactivated	1.266	0.96
IL1	1.023	0.65
Rapamycin	0.657	1.096
Tcell	0.896	-0.137
GMCSF	1.766	0.869
IFNab	0.686	0.819
IFNg	1.406	1.676
IFNg_GMCSF1	0.0	0.918
Rv1432_day32	-1.042	-0.343
Rv1565c_day32	1.567	-0.321
secA2_input	0.18	0.0
delta_Rv3594	-0.529	-0.899
delta_Rv3717	-0.062	-0.008
delta_Rv3811	0.568	0.248
delta_Rv0954	-1.112	0.844
PonA1	-1.602	0.589
EccD1_KO	0.414	0.434
EspI_KO	1.198	-0.414
PE35_KO	0.84	0.184
PPE68_KO	0.771	0.278
glycerol2	0.717	1.145
lignocerate	1.492	2.056
oleate	-3.549	-3.077
phosphatidylcholine	0.378	0.431
acetate	1.197	2.519
glucAc	1.646	1.7
Rv0950ko	0.265	-0.597
Rv1096ko	0.09	0.0
Rv3684ko	-0.049	-1.539
delta_otsA_trehalose	0.111	0.999