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 Rv1204c/-:

update plot	correlation	link to info on gene
Rv1205/-	(cc=0.4958)	info on Rv1205/-
Rv0539/-	(cc=0.4727)	info on Rv0539/-
Rv2426c/-	(cc=0.4346)	info on Rv2426c/-
Rv1071c/echA9	(cc=0.4318)	info on Rv1071c/echA9
Rv1206/fadD6	(cc=0.4205)	info on Rv1206/fadD6
Rv3463/-	(cc=0.4158)	info on Rv3463/-
Rv1151c/-	(cc=0.3926)	info on Rv1151c/-
Rv0393/-	(cc=0.3923)	info on Rv0393/-
Rv2550c/vapB20	(cc=0.3916)	info on Rv2550c/vapB20
Rv2656c/-	(cc=0.391)	info on Rv2656c/-

Correlation of Rv1204c/- with Rv2656c/-

Normalized LFCs for Rv1204c/-:
(description and provenance of datasets)

	Rv1204c/-	Rv2656c/-
Fe_supp_jason_reseq	-0.838	-0.043
low_pH_jason_reseq	0.438	0.045
NO_jason_reseq	0.299	1.738
B6_jason_reseq	0.67	1.599
MHCII_jason_reseq	-0.108	0.99
Isoniazid02	-0.231	0.354
Rifampicin4	0.092	0.39
Ethambutol3	2.259	2.977
Meropenem3	-0.092	0.139
Vancomycin16	-0.204	0.04
Rv2680_day32	-0.836	0.658
H37Rv_KO_MarP	-0.179	0.107
hypoxia_3wks	-0.77	-0.801
hypoxia_6wks	0.355	0.121
glycerol	0.105	1.04
cholesterol	0.025	0.209
AJ	0.225	1.768
Bibs02	-1.424	0.042
Bibs02c	0.427	-0.221
BL6	0.626	0.18
BL6a	0.103	0.573
BXD01	0.38	1.882
BXD010	0.155	1.409
BXD011	0.017	2.756
BXD03	0.593	1.517
BXD04	0.909	2.194
BXD05	-0.086	2.084
BXD06	0.113	1.44
BXD07	0.134	1.547
BXD08	0.625	1.072
BXD09	-0.063	1.736
CAST	1.405	3.48
CCcont	-0.182	0.606
DS01	0.76	0.108
DS02	0.211	0.099
DS04	0.878	1.158
DS0c	0.13	1.023
GP01	-1.315	-0.707
GP02	-0.203	-1.661
GP0c	-0.158	-0.291
NOD	-0.05	1.103
NZO	-0.204	1.699
PWK	0.922	1.8
H37Rv_KO_CtpC	0.921	2.318
H37Rv_KO_CtpD	0.537	1.646
H37Rv_KO_Rv1272	0.154	1.626
H37Rv_KO_SugABC	0.302	1.237
H37Rv_KO_MbtN	-0.116	-0.55
Trans05	0.458	2.493
macrophage_unactivated	-0.679	0.347
IL1	-0.344	1.593
Rapamycin	-0.396	0.534
Tcell	0.169	0.541
GMCSF	0.016	0.158
IFNab	0.018	1.058
IFNg	-0.556	1.371
IFNg_GMCSF1	-0.075	1.207
Rv1432_day32	-0.395	0.207
Rv1565c_day32	-0.686	0.054
secA2_input	0.6	1.119
delta_Rv3594	0.207	-0.974
delta_Rv3717	0.52	-1.013
delta_Rv3811	-0.396	-1.423
delta_Rv0954	0.93	-0.204
PonA1	0.394	-0.652
EccD1_KO	1.414	2.345
EspI_KO	-0.177	0.416
PE35_KO	0.198	0.201
PPE68_KO	-0.141	1.449
glycerol2	0.687	-0.168
lignocerate	1.101	0.472
oleate	0.712	-0.841
phosphatidylcholine	1.373	0.123
acetate	0.746	0.806
glucAc	0.247	0.641
Rv0950ko	0.353	-0.259
Rv1096ko	0.443	-1.258
Rv3684ko	-0.75	-1.087
delta_otsA_trehalose	-0.159	0.114