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 Rv3254/-:

update plot	correlation	link to info on gene
Rv1472/echA12	(cc=0.5954)	info on Rv1472/echA12
Rv1356c/-	(cc=0.5214)	info on Rv1356c/-
Rv1856c/-	(cc=0.4477)	info on Rv1856c/-
Rv2809/-	(cc=0.4041)	info on Rv2809/-
Rv2939/papA5	(cc=0.4003)	info on Rv2939/papA5
Rv2930/fadD26	(cc=0.398)	info on Rv2930/fadD26
Rv2935/ppsE	(cc=0.3927)	info on Rv2935/ppsE
Rv1703c/-	(cc=0.388)	info on Rv1703c/-
Rv2934/ppsD	(cc=0.3828)	info on Rv2934/ppsD
Rv2287/yjcE	(cc=0.3819)	info on Rv2287/yjcE

Correlation of Rv3254/- with Rv1356c/-

Normalized LFCs for Rv3254/-:
(description and provenance of datasets)

	Rv3254/-	Rv1356c/-
Fe_supp_jason_reseq	-0.456	0.805
low_pH_jason_reseq	-0.08	-0.214
NO_jason_reseq	0.903	-0.478
B6_jason_reseq	-0.289	0.18
MHCII_jason_reseq	0.926	0.023
Isoniazid02	0.019	1.425
Rifampicin4	-0.517	0.217
Ethambutol3	0.288	1.228
Meropenem3	0.25	0.12
Vancomycin16	-0.255	0.414
Rv2680_day32	-0.491	-0.561
H37Rv_KO_MarP	0.226	-0.047
hypoxia_3wks	-0.032	0.291
hypoxia_6wks	0.217	0.299
glycerol	-0.401	-0.705
cholesterol	0.015	-0.077
AJ	0.494	-0.187
Bibs02	0.433	-0.024
Bibs02c	-0.353	0.182
BL6	0.365	-0.066
BL6a	0.039	0.352
BXD01	-0.463	-0.087
BXD010	-0.149	-0.158
BXD011	-0.35	0.111
BXD03	0.42	-0.547
BXD04	0.318	0.298
BXD05	0.218	-0.47
BXD06	-0.241	-0.107
BXD07	-0.028	-0.56
BXD08	-0.09	-0.243
BXD09	0.148	0.171
CAST	-0.012	0.0
CCcont	0.037	-0.418
DS01	0.116	-0.125
DS02	0.287	-0.236
DS04	-0.433	0.814
DS0c	0.38	0.289
GP01	0.771	0.689
GP02	0.087	1.014
GP0c	-0.251	0.0
NOD	0.706	0.696
NZO	0.77	0.026
PWK	0.077	0.026
H37Rv_KO_CtpC	0.339	0.271
H37Rv_KO_CtpD	0.417	0.225
H37Rv_KO_Rv1272	0.938	0.555
H37Rv_KO_SugABC	0.39	1.183
H37Rv_KO_MbtN	0.591	-1.266
Trans05	0.257	1.178
macrophage_unactivated	2.591	1.048
IL1	-1.068	-3.601
Rapamycin	-0.654	-2.704
Tcell	2.597	4.259
GMCSF	0.407	-3.057
IFNab	-0.46	-2.875
IFNg	-1.045	-2.061
IFNg_GMCSF1	-0.396	-1.741
Rv1432_day32	-0.447	-0.172
Rv1565c_day32	0.243	-1.717
secA2_input	0.011	-0.7
delta_Rv3594	0.165	0.323
delta_Rv3717	0.026	-0.107
delta_Rv3811	-0.174	0.586
delta_Rv0954	-0.646	0.509
PonA1	-0.6	0.159
EccD1_KO	0.243	0.704
EspI_KO	0.368	0.841
PE35_KO	0.904	0.624
PPE68_KO	1.184	0.685
glycerol2	-0.038	-0.024
lignocerate	0.487	0.1
oleate	0.111	0.184
phosphatidylcholine	0.406	0.246
acetate	0.066	0.028
glucAc	-0.108	-0.289
Rv0950ko	-0.621	-0.042
Rv1096ko	-0.112	-0.721
Rv3684ko	-0.223	-0.783
delta_otsA_trehalose	0.75	0.814