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 Rv3906c/-:

update plot	correlation	link to info on gene
Rv2059/-	(cc=0.5571)	info on Rv2059/-
Rv1697/-	(cc=0.5534)	info on Rv1697/-
Rv2712c/-	(cc=0.5133)	info on Rv2712c/-
Rv0325/-	(cc=0.4769)	info on Rv0325/-
Rv1688/mpg	(cc=0.4757)	info on Rv1688/mpg
Rv2332/mez	(cc=0.4704)	info on Rv2332/mez
Rv2333c/stp	(cc=0.4659)	info on Rv2333c/stp
Rv2681/-	(cc=0.4562)	info on Rv2681/-
Rv3136A/-	(cc=0.453)	info on Rv3136A/-
Rv0532/PE_PGRS6	(cc=0.4519)	info on Rv0532/PE_PGRS6

Correlation of Rv3906c/- with Rv2059/-

Normalized LFCs for Rv3906c/-:
(description and provenance of datasets)

	Rv3906c/-	Rv2059/-
Fe_supp_jason_reseq	-0.448	0.262
low_pH_jason_reseq	0.478	-0.269
NO_jason_reseq	0.814	0.252
B6_jason_reseq	-0.396	0.517
MHCII_jason_reseq	-0.074	0.108
Isoniazid02	4.598	1.976
Rifampicin4	1.004	1.021
Ethambutol3	1.086	2.309
Meropenem3	0.138	0.0
Vancomycin16	0.409	-0.162
Rv2680_day32	-0.563	0.597
H37Rv_KO_MarP	0.542	-0.167
hypoxia_3wks	0.068	0.0
hypoxia_6wks	0.677	0.743
glycerol	-0.468	-1.053
cholesterol	-0.711	-0.931
AJ	-0.198	1.008
Bibs02	-0.658	-0.06
Bibs02c	-0.711	-0.767
BL6	-0.684	-0.359
BL6a	-1.745	-0.459
BXD01	-0.66	-0.101
BXD010	-1.201	-0.358
BXD011	-1.039	-0.237
BXD03	-1.191	-1.1
BXD04	0.675	0.262
BXD05	-0.336	-0.6
BXD06	-0.527	0.129
BXD07	-0.702	-0.572
BXD08	-0.443	-0.308
BXD09	-0.913	-0.28
CAST	0.152	-0.357
CCcont	-0.768	-0.367
DS01	0.477	-0.308
DS02	0.359	-0.476
DS04	0.765	0.493
DS0c	-0.085	0.352
GP01	-0.774	-0.165
GP02	-0.098	0.356
GP0c	-0.442	0.034
NOD	0.334	0.083
NZO	0.65	-0.11
PWK	1.114	0.364
H37Rv_KO_CtpC	-0.131	0.109
H37Rv_KO_CtpD	0.054	0.733
H37Rv_KO_Rv1272	-0.379	0.376
H37Rv_KO_SugABC	0.291	0.756
H37Rv_KO_MbtN	0.361	-0.212
Trans05	-0.652	0.947
macrophage_unactivated	-0.562	-0.268
IL1	-0.323	-0.139
Rapamycin	1.224	0.454
Tcell	-0.938	-0.121
GMCSF	-0.565	0.143
IFNab	-0.502	-0.438
IFNg	0.027	-0.414
IFNg_GMCSF1	0.223	-0.236
Rv1432_day32	-0.145	-0.065
Rv1565c_day32	0.54	0.374
secA2_input	-0.49	0.427
delta_Rv3594	-1.423	-0.289
delta_Rv3717	-0.774	-0.084
delta_Rv3811	-0.757	-0.503
delta_Rv0954	-0.942	-0.559
PonA1	0.811	-0.038
EccD1_KO	0.23	-0.138
EspI_KO	0.0	0.023
PE35_KO	0.379	-0.023
PPE68_KO	0.09	-0.026
glycerol2	0.82	-0.298
lignocerate	0.324	0.207
oleate	0.441	-0.522
phosphatidylcholine	0.099	0.025
acetate	1.032	-0.123
glucAc	-0.191	-0.028
Rv0950ko	-0.286	0.362
Rv1096ko	-0.648	-0.054
Rv3684ko	0.0	-0.118
delta_otsA_trehalose	-0.071	-0.136