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 Rv3039c/echA17:

update plot	correlation	link to info on gene
Rv0781/ptrBa	(cc=0.4406)	info on Rv0781/ptrBa
Rv0427c/xthA	(cc=0.4258)	info on Rv0427c/xthA
Rv0948c/-	(cc=0.423)	info on Rv0948c/-
Rv1114/vapC32	(cc=0.4088)	info on Rv1114/vapC32
Rv2767c/-	(cc=0.4001)	info on Rv2767c/-
Rv2290/lppO	(cc=0.3994)	info on Rv2290/lppO
Rv1869c/-	(cc=0.3929)	info on Rv1869c/-
Rv1233c/-	(cc=0.3912)	info on Rv1233c/-
Rv0553/menC	(cc=0.3836)	info on Rv0553/menC
Rv3189/-	(cc=0.3816)	info on Rv3189/-

Correlation of Rv3039c/echA17 with Rv1869c/-

Normalized LFCs for Rv3039c/echA17:
(description and provenance of datasets)

	Rv3039c/echA17	Rv1869c/-
Fe_supp_jason_reseq	-0.923	0.013
low_pH_jason_reseq	-2.652	-0.112
NO_jason_reseq	0.457	0.27
B6_jason_reseq	0.461	0.14
MHCII_jason_reseq	1.475	0.812
Isoniazid02	0.767	0.447
Rifampicin4	-1.202	-0.33
Ethambutol3	0.0	0.34
Meropenem3	0.146	1.387
Vancomycin16	-0.231	0.066
Rv2680_day32	2.205	0.525
H37Rv_KO_MarP	0.363	0.157
hypoxia_3wks	-0.128	0.0
hypoxia_6wks	0.37	0.443
glycerol	-1.24	-0.661
cholesterol	0.233	-0.725
AJ	0.938	0.449
Bibs02	-1.325	-0.029
Bibs02c	1.69	0.32
BL6	0.321	-0.132
BL6a	2.177	0.518
BXD01	0.242	-0.108
BXD010	1.779	0.397
BXD011	1.263	0.444
BXD03	0.0	0.09
BXD04	0.199	0.172
BXD05	1.773	0.51
BXD06	0.824	0.141
BXD07	1.209	0.237
BXD08	0.71	0.417
BXD09	1.425	0.379
CAST	0.254	0.33
CCcont	0.797	-0.267
DS01	1.42	0.339
DS02	-0.572	0.282
DS04	-1.093	0.159
DS0c	0.605	0.046
GP01	-1.322	-0.117
GP02	-1.114	-0.103
GP0c	-1.19	-0.618
NOD	-0.508	-0.011
NZO	0.767	0.42
PWK	-0.918	0.72
H37Rv_KO_CtpC	-1.729	-0.271
H37Rv_KO_CtpD	-1.348	0.557
H37Rv_KO_Rv1272	-1.747	0.475
H37Rv_KO_SugABC	-0.978	0.357
H37Rv_KO_MbtN	-0.747	0.022
Trans05	-1.619	0.405
macrophage_unactivated	-0.133	-0.786
IL1	0.356	-0.092
Rapamycin	1.126	0.095
Tcell	-0.818	-0.837
GMCSF	0.705	-0.288
IFNab	0.305	0.272
IFNg	0.665	-0.016
IFNg_GMCSF1	0.129	0.135
Rv1432_day32	0.0	0.098
Rv1565c_day32	1.151	-1.27
secA2_input	1.368	-0.153
delta_Rv3594	1.127	0.541
delta_Rv3717	0.707	0.023
delta_Rv3811	1.903	0.495
delta_Rv0954	0.398	0.253
PonA1	-0.56	0.132
EccD1_KO	1.23	0.812
EspI_KO	1.914	0.796
PE35_KO	0.58	0.624
PPE68_KO	1.814	0.893
glycerol2	-0.761	-0.398
lignocerate	-0.874	-0.326
oleate	-0.89	-0.242
phosphatidylcholine	-1.14	-0.375
acetate	-1.807	-0.421
glucAc	-0.949	-0.648
Rv0950ko	-0.112	-0.151
Rv1096ko	0.323	-0.609
Rv3684ko	0.35	-0.275
delta_otsA_trehalose	0.322	1.056