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 Rv2389c/rpfD:

update plot	correlation	link to info on gene
Rv3531c/-	(cc=0.5756)	info on Rv3531c/-
Rv0149/-	(cc=0.5136)	info on Rv0149/-
Rv3398c/idsA1	(cc=0.513)	info on Rv3398c/idsA1
Rv1131/prpC	(cc=0.5045)	info on Rv1131/prpC
Rv1817/-	(cc=0.5017)	info on Rv1817/-
Rv1482c/-	(cc=0.4939)	info on Rv1482c/-
Rv3016/lpqA	(cc=0.4862)	info on Rv3016/lpqA
Rv2041c/-	(cc=0.4743)	info on Rv2041c/-
Rv2704/-	(cc=0.4731)	info on Rv2704/-
Rv2113/-	(cc=0.473)	info on Rv2113/-

Correlation of Rv2389c/rpfD with Rv3531c/-

Normalized LFCs for Rv2389c/rpfD:
(description and provenance of datasets)

	Rv2389c/rpfD	Rv3531c/-
Fe_supp_jason_reseq	-0.362	-1.263
low_pH_jason_reseq	-0.435	-0.761
NO_jason_reseq	0.197	0.27
B6_jason_reseq	-0.716	-1.317
MHCII_jason_reseq	-0.625	-0.798
Isoniazid02	0.086	-0.425
Rifampicin4	0.049	-0.829
Ethambutol3	-0.016	-0.422
Meropenem3	2.093	0.09
Vancomycin16	-0.064	-0.337
Rv2680_day32	0.647	0.544
H37Rv_KO_MarP	0.553	0.247
hypoxia_3wks	0.355	0.447
hypoxia_6wks	-0.019	0.478
glycerol	0.891	0.74
cholesterol	-0.168	-1.314
AJ	0.0	0.118
Bibs02	-0.17	-0.334
Bibs02c	0.435	0.417
BL6	0.489	0.263
BL6a	0.672	0.264
BXD01	-0.141	0.159
BXD010	0.577	0.41
BXD011	0.542	1.163
BXD03	0.242	0.7
BXD04	0.34	-0.134
BXD05	0.563	0.922
BXD06	0.173	0.85
BXD07	0.135	0.495
BXD08	-0.097	0.293
BXD09	0.337	0.577
CAST	0.135	0.0
CCcont	-0.29	-0.039
DS01	0.026	0.26
DS02	-0.047	-0.397
DS04	0.342	0.526
DS0c	-0.286	0.082
GP01	0.004	0.847
GP02	0.234	-0.321
GP0c	0.43	0.273
NOD	0.298	-0.181
NZO	-0.176	0.243
PWK	0.128	1.37
H37Rv_KO_CtpC	0.735	0.917
H37Rv_KO_CtpD	0.486	0.563
H37Rv_KO_Rv1272	1.233	0.452
H37Rv_KO_SugABC	0.781	0.926
H37Rv_KO_MbtN	0.418	0.149
Trans05	0.521	0.581
macrophage_unactivated	0.597	0.593
IL1	0.887	0.679
Rapamycin	1.148	0.703
Tcell	-0.994	0.114
GMCSF	0.969	1.241
IFNab	0.865	0.408
IFNg	1.264	0.094
IFNg_GMCSF1	1.458	0.782
Rv1432_day32	0.332	0.13
Rv1565c_day32	0.482	-0.578
secA2_input	-0.178	-0.695
delta_Rv3594	-0.202	-0.112
delta_Rv3717	-0.321	-0.361
delta_Rv3811	-0.586	-0.342
delta_Rv0954	-0.295	-0.428
PonA1	0.614	0.503
EccD1_KO	0.812	0.168
EspI_KO	0.633	-0.405
PE35_KO	0.534	0.292
PPE68_KO	0.195	0.563
glycerol2	-0.581	-0.979
lignocerate	-1.078	-1.011
oleate	0.302	-0.359
phosphatidylcholine	-0.294	-0.581
acetate	-1.282	-1.094
glucAc	-1.315	-0.701
Rv0950ko	0.443	-0.335
Rv1096ko	0.169	-1.128
Rv3684ko	0.144	-0.458
delta_otsA_trehalose	1.314	-0.176