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 Rv3854c/ethA:

update plot	correlation	link to info on gene
Rv1111c/-	(cc=0.69)	info on Rv1111c/-
Rv0049/-	(cc=0.6401)	info on Rv0049/-
Rv1633/uvrB	(cc=0.6285)	info on Rv1633/uvrB
Rv3818/-	(cc=0.6279)	info on Rv3818/-
Rv0497/-	(cc=0.6185)	info on Rv0497/-
Rv3050c/-	(cc=0.6182)	info on Rv3050c/-
Rv2735c/-	(cc=0.6143)	info on Rv2735c/-
Rv2190c/-	(cc=0.6139)	info on Rv2190c/-
Rv3218/-	(cc=0.6118)	info on Rv3218/-
Rv3125c/PPE49	(cc=0.6093)	info on Rv3125c/PPE49

Correlation of Rv3854c/ethA with Rv1633/uvrB

Normalized LFCs for Rv3854c/ethA:
(description and provenance of datasets)

	Rv3854c/ethA	Rv1633/uvrB
Fe_supp_jason_reseq	0.998	2.98
low_pH_jason_reseq	-0.467	0.507
NO_jason_reseq	0.683	-0.517
B6_jason_reseq	-0.283	-1.215
MHCII_jason_reseq	0.123	-0.73
Isoniazid02	-0.387	-0.648
Rifampicin4	-0.382	0.022
Ethambutol3	-0.039	0.067
Meropenem3	-0.346	-0.71
Vancomycin16	-0.767	-1.326
Rv2680_day32	0.22	-0.518
H37Rv_KO_MarP	-1.053	-0.563
hypoxia_3wks	-0.032	-2.743
hypoxia_6wks	-0.033	-2.575
glycerol	-0.385	1.565
cholesterol	0.709	0.932
AJ	-0.788	-0.124
Bibs02	0.201	0.348
Bibs02c	-0.092	0.958
BL6	0.606	1.479
BL6a	0.933	2.274
BXD01	0.281	1.401
BXD010	0.77	1.514
BXD011	0.723	2.168
BXD03	1.176	1.77
BXD04	0.639	1.523
BXD05	1.269	1.762
BXD06	1.119	1.844
BXD07	0.804	1.792
BXD08	0.326	1.572
BXD09	0.918	1.902
CAST	-0.247	-0.692
CCcont	0.588	3.594
DS01	0.275	0.12
DS02	0.391	0.318
DS04	0.188	0.888
DS0c	0.016	0.596
GP01	0.561	1.062
GP02	0.572	0.159
GP0c	0.787	2.173
NOD	-0.428	-1.199
NZO	0.272	-0.897
PWK	0.203	-0.732
H37Rv_KO_CtpC	0.506	2.151
H37Rv_KO_CtpD	1.09	2.17
H37Rv_KO_Rv1272	1.067	2.201
H37Rv_KO_SugABC	1.875	1.396
H37Rv_KO_MbtN	0.978	3.197
Trans05	0.77	1.691
macrophage_unactivated	0.492	0.792
IL1	0.169	-0.469
Rapamycin	0.107	0.15
Tcell	0.277	0.746
GMCSF	0.298	0.0
IFNab	0.257	1.817
IFNg	0.673	0.067
IFNg_GMCSF1	0.355	-0.408
Rv1432_day32	0.454	-0.617
Rv1565c_day32	-0.025	-0.706
secA2_input	0.288	1.027
delta_Rv3594	0.649	0.829
delta_Rv3717	1.076	0.982
delta_Rv3811	1.147	0.671
delta_Rv0954	0.171	0.178
PonA1	0.143	-0.372
EccD1_KO	0.253	-0.595
EspI_KO	-0.317	-0.248
PE35_KO	-0.615	-0.114
PPE68_KO	-0.109	-0.026
glycerol2	-0.493	-1.772
lignocerate	-0.235	-1.842
oleate	-0.179	-2.678
phosphatidylcholine	-0.43	-2.389
acetate	-0.321	-0.09
glucAc	-0.429	0.511
Rv0950ko	0.639	-0.383
Rv1096ko	0.274	-0.208
Rv3684ko	0.874	-0.295
delta_otsA_trehalose	-0.014	0.476