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 Rv2939/papA5

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

	Rv3254/-	Rv2939/papA5
Fe_supp_jason_reseq	-0.456	1.588
low_pH_jason_reseq	-0.08	1.822
NO_jason_reseq	0.903	-0.42
B6_jason_reseq	-0.289	0.953
MHCII_jason_reseq	0.926	-3.495
Isoniazid02	0.019	0.274
Rifampicin4	-0.517	0.753
Ethambutol3	0.288	0.378
Meropenem3	0.25	0.579
Vancomycin16	-0.255	0.143
Rv2680_day32	-0.491	-2.003
H37Rv_KO_MarP	0.226	0.09
hypoxia_3wks	-0.032	0.239
hypoxia_6wks	0.217	-0.716
glycerol	-0.401	2.5
cholesterol	0.015	2.136
AJ	0.494	0.617
Bibs02	0.433	-3.694
Bibs02c	-0.353	-3.575
BL6	0.365	0.191
BL6a	0.039	-0.918
BXD01	-0.463	1.501
BXD010	-0.149	0.097
BXD011	-0.35	-0.375
BXD03	0.42	0.135
BXD04	0.318	1.46
BXD05	0.218	-0.769
BXD06	-0.241	0.126
BXD07	-0.028	0.018
BXD08	-0.09	0.678
BXD09	0.148	0.054
CAST	-0.012	3.04
CCcont	0.037	1.053
DS01	0.116	0.453
DS02	0.287	0.945
DS04	-0.433	0.013
DS0c	0.38	0.112
GP01	0.771	-2.855
GP02	0.087	-2.322
GP0c	-0.251	-3.511
NOD	0.706	2.177
NZO	0.77	2.196
PWK	0.077	0.064
H37Rv_KO_CtpC	0.339	-1.209
H37Rv_KO_CtpD	0.417	0.317
H37Rv_KO_Rv1272	0.938	-0.465
H37Rv_KO_SugABC	0.39	0.991
H37Rv_KO_MbtN	0.591	0.116
Trans05	0.257	0.115
macrophage_unactivated	2.591	4.11
IL1	-1.068	-3.067
Rapamycin	-0.654	-2.968
Tcell	2.597	4.06
GMCSF	0.407	-3.535
IFNab	-0.46	-2.364
IFNg	-1.045	-4.327
IFNg_GMCSF1	-0.396	-0.443
Rv1432_day32	-0.447	-0.391
Rv1565c_day32	0.243	-2.357
secA2_input	0.011	-0.734
delta_Rv3594	0.165	-2.487
delta_Rv3717	0.026	-2.58
delta_Rv3811	-0.174	-2.538
delta_Rv0954	-0.646	-2.101
PonA1	-0.6	-1.645
EccD1_KO	0.243	-4.535
EspI_KO	0.368	-3.046
PE35_KO	0.904	2.438
PPE68_KO	1.184	0.275
glycerol2	-0.038	1.002
lignocerate	0.487	1.08
oleate	0.111	1.059
phosphatidylcholine	0.406	1.064
acetate	0.066	0.133
glucAc	-0.108	-0.177
Rv0950ko	-0.621	-4.095
Rv1096ko	-0.112	-5.805
Rv3684ko	-0.223	-3.439
delta_otsA_trehalose	0.75	-0.972