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 Rv0305c/PPE6:

update plot	correlation	link to info on gene
Rv1917c/PPE34	(cc=0.6677)	info on Rv1917c/PPE34
Rv1918c/PPE35	(cc=0.6401)	info on Rv1918c/PPE35
Rv2735c/-	(cc=0.6291)	info on Rv2735c/-
Rv1500/-	(cc=0.6116)	info on Rv1500/-
Rv2338c/moeW	(cc=0.6041)	info on Rv2338c/moeW
Rv3796/-	(cc=0.5975)	info on Rv3796/-
Rv2430c/PPE41	(cc=0.5849)	info on Rv2430c/PPE41
Rv3382c/lytB1	(cc=0.584)	info on Rv3382c/lytB1
Rv0469/umaA	(cc=0.5786)	info on Rv0469/umaA
Rv1585c/-	(cc=0.5774)	info on Rv1585c/-

Correlation of Rv0305c/PPE6 with Rv1917c/PPE34

Normalized LFCs for Rv0305c/PPE6:
(description and provenance of datasets)

	Rv0305c/PPE6	Rv1917c/PPE34
Fe_supp_jason_reseq	0.584	0.756
low_pH_jason_reseq	-0.248	-0.311
NO_jason_reseq	-0.333	0.15
B6_jason_reseq	-0.199	0.621
MHCII_jason_reseq	0.274	0.641
Isoniazid02	-0.374	0.063
Rifampicin4	0.133	0.173
Ethambutol3	0.022	0.472
Meropenem3	0.488	0.435
Vancomycin16	-0.255	0.0
Rv2680_day32	-0.065	0.08
H37Rv_KO_MarP	-0.106	-0.09
hypoxia_3wks	0.195	-0.327
hypoxia_6wks	-0.104	-0.048
glycerol	-0.252	-0.107
cholesterol	-0.306	0.128
AJ	0.506	0.57
Bibs02	0.13	0.162
Bibs02c	0.247	0.318
BL6	0.258	-0.053
BL6a	0.373	0.471
BXD01	0.345	0.587
BXD010	0.176	0.534
BXD011	0.352	0.557
BXD03	0.263	-0.042
BXD04	0.162	0.582
BXD05	0.679	0.634
BXD06	0.201	0.566
BXD07	0.145	0.283
BXD08	0.476	0.237
BXD09	0.364	0.465
CAST	0.611	0.489
CCcont	0.096	0.059
DS01	0.558	0.71
DS02	0.501	0.517
DS04	0.401	0.492
DS0c	0.46	0.368
GP01	0.546	0.503
GP02	0.609	0.523
GP0c	0.212	0.496
NOD	1.365	0.657
NZO	0.4	0.522
PWK	0.166	0.281
H37Rv_KO_CtpC	0.431	0.743
H37Rv_KO_CtpD	1.852	1.346
H37Rv_KO_Rv1272	1.229	1.285
H37Rv_KO_SugABC	1.067	1.237
H37Rv_KO_MbtN	0.798	0.899
Trans05	0.903	1.105
macrophage_unactivated	0.846	0.275
IL1	-0.208	-0.116
Rapamycin	0.0	-0.203
Tcell	0.925	0.44
GMCSF	0.275	0.325
IFNab	-0.151	-0.366
IFNg	0.561	0.035
IFNg_GMCSF1	0.06	-0.082
Rv1432_day32	0.026	0.139
Rv1565c_day32	-0.13	0.366
secA2_input	-0.621	-0.675
delta_Rv3594	0.0	0.503
delta_Rv3717	-0.39	0.072
delta_Rv3811	-0.097	0.363
delta_Rv0954	-0.465	-0.36
PonA1	0.045	-0.493
EccD1_KO	-0.743	-0.138
EspI_KO	-0.627	-0.12
PE35_KO	-0.642	-0.123
PPE68_KO	-0.598	-0.067
glycerol2	-0.136	0.303
lignocerate	-0.078	0.424
oleate	-0.138	0.289
phosphatidylcholine	0.011	0.641
acetate	-0.474	0.209
glucAc	-0.345	0.274
Rv0950ko	0.911	-0.187
Rv1096ko	-0.208	-0.841
Rv3684ko	0.098	-0.796
delta_otsA_trehalose	-0.191	-0.262