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 Rv2126c/PE_PGRS37:

update plot	correlation	link to info on gene
Rv2972c/-	(cc=0.5261)	info on Rv2972c/-
Rv2970A/-	(cc=0.4649)	info on Rv2970A/-
Rv2779c/-	(cc=0.4421)	info on Rv2779c/-
Rv3430c/-	(cc=0.4414)	info on Rv3430c/-
Rv1879/-	(cc=0.4323)	info on Rv1879/-
Rv1579c/-	(cc=0.4048)	info on Rv1579c/-
Rv3339c/icd1	(cc=0.3928)	info on Rv3339c/icd1
Rv0728c/serA2	(cc=0.3883)	info on Rv0728c/serA2
Rv3123/-	(cc=0.3877)	info on Rv3123/-
Rv1520/-	(cc=0.3711)	info on Rv1520/-

Correlation of Rv2126c/PE_PGRS37 with Rv2972c/-

Normalized LFCs for Rv2126c/PE_PGRS37:
(description and provenance of datasets)

	Rv2126c/PE_PGRS37	Rv2972c/-
Fe_supp_jason_reseq	0.257	0.723
low_pH_jason_reseq	-0.065	-0.95
NO_jason_reseq	-0.722	0.179
B6_jason_reseq	0.766	0.577
MHCII_jason_reseq	0.501	0.422
Isoniazid02	0.781	-0.019
Rifampicin4	0.853	-0.195
Ethambutol3	3.067	0.655
Meropenem3	1.497	1.458
Vancomycin16	0.799	0.464
Rv2680_day32	1.032	0.901
H37Rv_KO_MarP	-0.168	0.432
hypoxia_3wks	-0.494	-0.734
hypoxia_6wks	-0.829	-0.23
glycerol	-0.186	-1.128
cholesterol	-0.961	-0.347
AJ	0.615	0.469
Bibs02	0.64	-0.016
Bibs02c	0.997	-0.653
BL6	-0.048	0.362
BL6a	0.913	-0.009
BXD01	1.015	0.071
BXD010	-0.391	0.286
BXD011	1.425	0.729
BXD03	-0.482	-0.316
BXD04	1.608	-0.122
BXD05	0.507	0.495
BXD06	0.699	0.187
BXD07	0.693	-0.018
BXD08	0.98	0.586
BXD09	0.359	0.361
CAST	-1.268	-0.43
CCcont	-0.48	-0.22
DS01	-0.457	0.099
DS02	-0.083	0.019
DS04	0.814	0.228
DS0c	-0.42	0.126
GP01	-1.837	-0.85
GP02	-0.065	0.36
GP0c	-0.636	-0.429
NOD	-0.27	0.076
NZO	0.282	0.617
PWK	-0.35	0.389
H37Rv_KO_CtpC	-0.195	0.134
H37Rv_KO_CtpD	-0.84	0.124
H37Rv_KO_Rv1272	-0.776	-1.257
H37Rv_KO_SugABC	0.966	0.56
H37Rv_KO_MbtN	1.055	0.483
Trans05	-0.836	-0.371
macrophage_unactivated	-0.41	0.189
IL1	1.071	0.513
Rapamycin	0.896	1.228
Tcell	0.606	0.098
GMCSF	0.824	0.502
IFNab	0.396	0.916
IFNg	0.468	0.783
IFNg_GMCSF1	0.688	1.241
Rv1432_day32	0.284	-0.259
Rv1565c_day32	-0.93	-1.259
secA2_input	0.792	0.23
delta_Rv3594	-0.87	-0.057
delta_Rv3717	-0.614	0.464
delta_Rv3811	-0.226	0.623
delta_Rv0954	-1.244	-0.019
PonA1	-1.028	-0.008
EccD1_KO	-0.497	0.158
EspI_KO	0.2	0.781
PE35_KO	-0.213	0.446
PPE68_KO	-0.077	0.154
glycerol2	0.349	0.289
lignocerate	0.026	0.175
oleate	1.404	0.934
phosphatidylcholine	0.514	0.354
acetate	-0.256	-0.672
glucAc	-0.394	-0.652
Rv0950ko	-0.66	-0.1
Rv1096ko	-0.917	-0.256
Rv3684ko	-1.294	0.331
delta_otsA_trehalose	0.657	1.505