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 Rv3293/pcd:

update plot	correlation	link to info on gene
Rv2062c/cobN	(cc=0.4643)	info on Rv2062c/cobN
Rv0488/-	(cc=0.4558)	info on Rv0488/-
Rv0906/-	(cc=0.432)	info on Rv0906/-
Rv3600c/-	(cc=0.4256)	info on Rv3600c/-
Rv2260/-	(cc=0.4095)	info on Rv2260/-
Rv0399c/lpqK	(cc=0.406)	info on Rv0399c/lpqK
Rv1997/ctpF	(cc=0.4035)	info on Rv1997/ctpF
Rv0269c/-	(cc=0.4027)	info on Rv0269c/-
Rv3191c/-	(cc=0.4001)	info on Rv3191c/-
Rv3175/-	(cc=0.3983)	info on Rv3175/-

Correlation of Rv3293/pcd with Rv3191c/-

Normalized LFCs for Rv3293/pcd:
(description and provenance of datasets)

	Rv3293/pcd	Rv3191c/-
Fe_supp_jason_reseq	-0.624	-0.024
low_pH_jason_reseq	0.216	-0.37
NO_jason_reseq	0.339	-0.06
B6_jason_reseq	1.237	0.47
MHCII_jason_reseq	0.486	0.448
Isoniazid02	-1.072	-1.929
Rifampicin4	0.024	0.625
Ethambutol3	-0.989	-2.151
Meropenem3	-0.474	-0.361
Vancomycin16	-0.531	-0.907
Rv2680_day32	0.49	0.071
H37Rv_KO_MarP	-0.363	0.409
hypoxia_3wks	-1.037	-0.395
hypoxia_6wks	-0.52	-0.683
glycerol	-0.607	-0.176
cholesterol	-0.222	-0.111
AJ	-0.118	0.424
Bibs02	0.511	0.283
Bibs02c	0.859	0.57
BL6	-0.66	-0.065
BL6a	0.178	0.716
BXD01	-0.052	-0.167
BXD010	-0.038	0.178
BXD011	-0.682	0.436
BXD03	-0.033	0.247
BXD04	-0.397	0.221
BXD05	-0.294	0.692
BXD06	0.033	0.452
BXD07	-0.099	0.158
BXD08	0.0	0.253
BXD09	-0.508	0.623
CAST	0.185	0.439
CCcont	-0.429	0.151
DS01	0.849	0.862
DS02	0.356	0.285
DS04	0.156	1.062
DS0c	-0.284	0.292
GP01	-0.24	0.304
GP02	-0.586	-0.484
GP0c	0.146	-0.684
NOD	-0.69	0.539
NZO	-1.169	0.585
PWK	-0.602	0.624
H37Rv_KO_CtpC	0.448	0.291
H37Rv_KO_CtpD	0.537	0.08
H37Rv_KO_Rv1272	-0.274	0.547
H37Rv_KO_SugABC	0.239	0.526
H37Rv_KO_MbtN	0.252	0.429
Trans05	0.112	0.094
macrophage_unactivated	-0.234	-0.174
IL1	-0.11	-0.047
Rapamycin	0.163	-0.169
Tcell	-0.56	-0.606
GMCSF	0.116	0.013
IFNab	-0.224	0.287
IFNg	-0.516	0.102
IFNg_GMCSF1	0.085	0.33
Rv1432_day32	0.945	0.316
Rv1565c_day32	0.542	-0.591
secA2_input	0.014	-0.632
delta_Rv3594	-0.806	-0.08
delta_Rv3717	0.093	-0.216
delta_Rv3811	-0.813	0.025
delta_Rv0954	-0.669	-0.26
PonA1	-0.563	0.123
EccD1_KO	0.178	-0.217
EspI_KO	0.605	0.371
PE35_KO	-0.053	0.082
PPE68_KO	-0.147	-0.189
glycerol2	-0.286	-0.113
lignocerate	0.0	0.516
oleate	-0.147	-0.413
phosphatidylcholine	-0.097	0.084
acetate	0.69	0.57
glucAc	0.601	0.485
Rv0950ko	0.392	0.109
Rv1096ko	1.493	0.38
Rv3684ko	0.357	0.301
delta_otsA_trehalose	-0.461	-0.138