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 Rv3339c/icd1

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

	Rv2126c/PE_PGRS37	Rv3339c/icd1
Fe_supp_jason_reseq	0.257	0.103
low_pH_jason_reseq	-0.065	0.661
NO_jason_reseq	-0.722	0.856
B6_jason_reseq	0.766	0.323
MHCII_jason_reseq	0.501	-0.011
Isoniazid02	0.781	-0.38
Rifampicin4	0.853	0.208
Ethambutol3	3.067	1.816
Meropenem3	1.497	0.192
Vancomycin16	0.799	0.13
Rv2680_day32	1.032	0.658
H37Rv_KO_MarP	-0.168	0.387
hypoxia_3wks	-0.494	-0.315
hypoxia_6wks	-0.829	-0.144
glycerol	-0.186	0.0
cholesterol	-0.961	0.121
AJ	0.615	0.6
Bibs02	0.64	0.265
Bibs02c	0.997	1.164
BL6	-0.048	0.143
BL6a	0.913	0.946
BXD01	1.015	0.548
BXD010	-0.391	0.251
BXD011	1.425	0.38
BXD03	-0.482	-0.227
BXD04	1.608	0.377
BXD05	0.507	0.143
BXD06	0.699	0.372
BXD07	0.693	0.583
BXD08	0.98	0.152
BXD09	0.359	0.326
CAST	-1.268	0.804
CCcont	-0.48	0.0
DS01	-0.457	0.659
DS02	-0.083	0.411
DS04	0.814	0.281
DS0c	-0.42	0.198
GP01	-1.837	-0.283
GP02	-0.065	0.063
GP0c	-0.636	0.388
NOD	-0.27	0.919
NZO	0.282	-0.017
PWK	-0.35	-0.141
H37Rv_KO_CtpC	-0.195	1.252
H37Rv_KO_CtpD	-0.84	1.067
H37Rv_KO_Rv1272	-0.776	0.748
H37Rv_KO_SugABC	0.966	1.045
H37Rv_KO_MbtN	1.055	0.782
Trans05	-0.836	-0.058
macrophage_unactivated	-0.41	0.855
IL1	1.071	0.036
Rapamycin	0.896	0.114
Tcell	0.606	0.534
GMCSF	0.824	0.346
IFNab	0.396	0.112
IFNg	0.468	-0.136
IFNg_GMCSF1	0.688	0.038
Rv1432_day32	0.284	1.538
Rv1565c_day32	-0.93	0.278
secA2_input	0.792	-0.441
delta_Rv3594	-0.87	-0.45
delta_Rv3717	-0.614	-0.693
delta_Rv3811	-0.226	-0.626
delta_Rv0954	-1.244	-1.433
PonA1	-1.028	-1.36
EccD1_KO	-0.497	-0.309
EspI_KO	0.2	0.026
PE35_KO	-0.213	-0.505
PPE68_KO	-0.077	0.058
glycerol2	0.349	-0.181
lignocerate	0.026	-0.348
oleate	1.404	0.01
phosphatidylcholine	0.514	-0.255
acetate	-0.256	-1.036
glucAc	-0.394	-0.59
Rv0950ko	-0.66	-0.13
Rv1096ko	-0.917	-0.13
Rv3684ko	-1.294	-0.586
delta_otsA_trehalose	0.657	0.009