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 Rv2408/PE24:

update plot	correlation	link to info on gene
Rv2577/-	(cc=0.56)	info on Rv2577/-
Rv2459/-	(cc=0.5404)	info on Rv2459/-
Rv1038c/esxJ	(cc=0.4985)	info on Rv1038c/esxJ
Rv2875/mpt70	(cc=0.4955)	info on Rv2875/mpt70
Rv2409c/-	(cc=0.4818)	info on Rv2409c/-
Rv2634c/PE_PGRS46	(cc=0.4728)	info on Rv2634c/PE_PGRS46
Rv0873/fadE10	(cc=0.4723)	info on Rv0873/fadE10
Rv3192/-	(cc=0.4637)	info on Rv3192/-
Rv1704c/cycA	(cc=0.4625)	info on Rv1704c/cycA
Rv0754/PE_PGRS11	(cc=0.4594)	info on Rv0754/PE_PGRS11

Correlation of Rv2408/PE24 with Rv0873/fadE10

Normalized LFCs for Rv2408/PE24:
(description and provenance of datasets)

	Rv2408/PE24	Rv0873/fadE10
Fe_supp_jason_reseq	0.385	0.892
low_pH_jason_reseq	-1.752	-1.044
NO_jason_reseq	-1.016	-0.732
B6_jason_reseq	-0.122	0.425
MHCII_jason_reseq	0.741	0.675
Isoniazid02	-0.696	-0.908
Rifampicin4	-0.198	0.341
Ethambutol3	-0.822	-0.111
Meropenem3	-0.979	-0.593
Vancomycin16	-0.462	-0.525
Rv2680_day32	-0.037	0.514
H37Rv_KO_MarP	0.413	0.306
hypoxia_3wks	-0.195	-0.251
hypoxia_6wks	-0.587	0.186
glycerol	0.051	0.184
cholesterol	0.357	0.542
AJ	-0.113	-0.178
Bibs02	0.062	-0.282
Bibs02c	-0.065	0.673
BL6	0.094	0.014
BL6a	0.026	0.485
BXD01	-0.1	0.187
BXD010	-0.147	-0.229
BXD011	-0.366	-0.084
BXD03	-0.228	-0.209
BXD04	0.161	0.271
BXD05	0.155	0.411
BXD06	-0.128	0.055
BXD07	-0.249	0.113
BXD08	0.314	0.251
BXD09	-0.26	-0.015
CAST	-0.437	-0.34
CCcont	0.206	-0.065
DS01	-0.214	0.394
DS02	0.038	0.487
DS04	-0.042	0.08
DS0c	-0.526	0.448
GP01	0.382	0.584
GP02	0.773	1.007
GP0c	-0.26	0.131
NOD	0.086	-0.387
NZO	-0.062	0.123
PWK	-0.476	-0.185
H37Rv_KO_CtpC	0.035	-0.342
H37Rv_KO_CtpD	0.61	0.489
H37Rv_KO_Rv1272	0.404	0.61
H37Rv_KO_SugABC	-1.885	0.11
H37Rv_KO_MbtN	-0.428	0.058
Trans05	-0.041	-0.131
macrophage_unactivated	-0.193	0.253
IL1	0.475	-0.374
Rapamycin	0.565	-0.285
Tcell	-0.088	0.072
GMCSF	-0.539	0.341
IFNab	-0.254	-0.209
IFNg	0.158	0.139
IFNg_GMCSF1	-0.393	-0.396
Rv1432_day32	1.288	0.175
Rv1565c_day32	0.063	-0.708
secA2_input	0.393	-0.131
delta_Rv3594	-0.021	0.459
delta_Rv3717	-0.638	0.0
delta_Rv3811	-0.107	0.446
delta_Rv0954	0.245	0.377
PonA1	-0.074	0.521
EccD1_KO	1.125	0.28
EspI_KO	0.819	0.67
PE35_KO	1.286	0.137
PPE68_KO	0.851	0.0
glycerol2	0.8	0.46
lignocerate	1.162	0.201
oleate	0.53	0.6
phosphatidylcholine	0.866	0.51
acetate	0.131	-0.298
glucAc	0.503	-0.621
Rv0950ko	0.449	0.021
Rv1096ko	-0.253	-0.486
Rv3684ko	-0.825	-0.501
delta_otsA_trehalose	0.527	0.97