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 Rv3125c/PPE49

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

	Rv3854c/ethA	Rv3125c/PPE49
Fe_supp_jason_reseq	0.998	0.477
low_pH_jason_reseq	-0.467	-0.905
NO_jason_reseq	0.683	-0.341
B6_jason_reseq	-0.283	-0.782
MHCII_jason_reseq	0.123	-0.117
Isoniazid02	-0.387	-1.523
Rifampicin4	-0.382	0.601
Ethambutol3	-0.039	-0.043
Meropenem3	-0.346	-0.69
Vancomycin16	-0.767	-0.401
Rv2680_day32	0.22	0.166
H37Rv_KO_MarP	-1.053	0.416
hypoxia_3wks	-0.032	0.156
hypoxia_6wks	-0.033	-0.301
glycerol	-0.385	-0.758
cholesterol	0.709	-0.625
AJ	-0.788	-0.407
Bibs02	0.201	-0.477
Bibs02c	-0.092	-0.565
BL6	0.606	0.71
BL6a	0.933	0.591
BXD01	0.281	0.585
BXD010	0.77	0.68
BXD011	0.723	0.847
BXD03	1.176	0.866
BXD04	0.639	0.919
BXD05	1.269	1.016
BXD06	1.119	0.893
BXD07	0.804	0.858
BXD08	0.326	0.984
BXD09	0.918	0.923
CAST	-0.247	-0.404
CCcont	0.588	0.879
DS01	0.275	-0.524
DS02	0.391	-0.102
DS04	0.188	-0.322
DS0c	0.016	-0.137
GP01	0.561	-0.031
GP02	0.572	0.54
GP0c	0.787	-0.314
NOD	-0.428	-0.034
NZO	0.272	-0.98
PWK	0.203	-0.206
H37Rv_KO_CtpC	0.506	0.68
H37Rv_KO_CtpD	1.09	1.285
H37Rv_KO_Rv1272	1.067	0.806
H37Rv_KO_SugABC	1.875	1.266
H37Rv_KO_MbtN	0.978	0.88
Trans05	0.77	0.694
macrophage_unactivated	0.492	-0.126
IL1	0.169	-0.208
Rapamycin	0.107	-0.365
Tcell	0.277	-0.326
GMCSF	0.298	-0.137
IFNab	0.257	-0.396
IFNg	0.673	-0.045
IFNg_GMCSF1	0.355	0.493
Rv1432_day32	0.454	-0.063
Rv1565c_day32	-0.025	-0.232
secA2_input	0.288	-0.567
delta_Rv3594	0.649	0.347
delta_Rv3717	1.076	0.193
delta_Rv3811	1.147	0.454
delta_Rv0954	0.171	-0.619
PonA1	0.143	-0.02
EccD1_KO	0.253	0.355
EspI_KO	-0.317	0.191
PE35_KO	-0.615	0.292
PPE68_KO	-0.109	0.054
glycerol2	-0.493	-0.175
lignocerate	-0.235	-0.373
oleate	-0.179	-0.034
phosphatidylcholine	-0.43	-0.269
acetate	-0.321	-0.595
glucAc	-0.429	-0.52
Rv0950ko	0.639	0.35
Rv1096ko	0.274	0.06
Rv3684ko	0.874	-0.157
delta_otsA_trehalose	-0.014	-1.215