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 Rv1080c/greA:

update plot	correlation	link to info on gene
Rv0541c/-	(cc=0.7621)	info on Rv0541c/-
Rv1078/pra	(cc=0.7002)	info on Rv1078/pra
Rv2553c/-	(cc=0.6866)	info on Rv2553c/-
Rv1836c/-	(cc=0.679)	info on Rv1836c/-
Rv2246/kasB	(cc=0.674)	info on Rv2246/kasB
Rv1340/rphA	(cc=0.659)	info on Rv1340/rphA
Rv0238/-	(cc=0.6578)	info on Rv0238/-
Rv1512/epiA	(cc=0.6488)	info on Rv1512/epiA
Rv3789/-	(cc=0.6464)	info on Rv3789/-
Rv2837c/-	(cc=0.6302)	info on Rv2837c/-

Correlation of Rv1080c/greA with Rv1340/rphA

Normalized LFCs for Rv1080c/greA:
(description and provenance of datasets)

	Rv1080c/greA	Rv1340/rphA
Fe_supp_jason_reseq	1.121	1.209
low_pH_jason_reseq	-0.231	0.231
NO_jason_reseq	0.633	0.0
B6_jason_reseq	0.267	0.0
MHCII_jason_reseq	-0.135	0.135
Isoniazid02	-0.851	1.053
Rifampicin4	-0.271	-1.939
Ethambutol3	0.505	0.146
Meropenem3	-0.12	0.0
Vancomycin16	-0.546	1.382
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-2.138	-2.822
hypoxia_3wks	-0.55	-0.427
hypoxia_6wks	0.503	1.748
glycerol	-0.385	2.017
cholesterol	0.233	0.0
AJ	0.193	0.0
Bibs02	-0.167	0.0
Bibs02c	-0.399	0.0
BL6	-0.114	0.0
BL6a	0.319	0.198
BXD01	-0.119	0.0
BXD010	0.299	0.0
BXD011	0.383	0.626
BXD03	-0.123	0.664
BXD04	0.199	0.34
BXD05	0.57	0.135
BXD06	0.0	0.254
BXD07	0.0	0.0
BXD08	0.111	0.0
BXD09	0.117	0.386
CAST	-0.21	0.0
CCcont	1.481	1.955
DS01	-0.216	0.0
DS02	-0.414	0.0
DS04	0.312	0.533
DS0c	0.349	0.0
GP01	0.672	0.0
GP02	-0.159	0.0
GP0c	0.551	0.0
NOD	0.361	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.261	0.0
H37Rv_KO_CtpD	0.381	0.0
H37Rv_KO_Rv1272	-0.129	0.0
H37Rv_KO_SugABC	0.083	0.768
H37Rv_KO_MbtN	2.002	0.0
Trans05	0.889	0.0
macrophage_unactivated	0.436	0.739
IL1	0.0	2.136
Rapamycin	0.0	1.525
Tcell	0.0	0.0
GMCSF	0.0	0.422
IFNab	0.0	-0.263
IFNg	0.0	0.994
IFNg_GMCSF1	0.0	0.958
Rv1432_day32	1.068	0.0
Rv1565c_day32	0.218	0.0
secA2_input	-0.348	-1.13
delta_Rv3594	3.356	1.579
delta_Rv3717	3.97	2.287
delta_Rv3811	3.554	0.934
delta_Rv0954	-2.225	-1.47
PonA1	-1.428	-0.583
EccD1_KO	-3.029	-3.924
EspI_KO	-1.825	-2.852
PE35_KO	-1.747	0.128
PPE68_KO	-0.755	-0.454
glycerol2	0.0	-1.188
lignocerate	0.0	-1.033
oleate	0.0	-1.202
phosphatidylcholine	0.0	-1.188
acetate	0.0	0.973
glucAc	0.0	-0.375
Rv0950ko	-3.35	-3.217
Rv1096ko	-1.888	-2.289
Rv3684ko	-0.655	-2.862
delta_otsA_trehalose	0.906	0.232