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 Rv0590/mce2B:

update plot	correlation	link to info on gene
Rv1153c/omt	(cc=0.5438)	info on Rv1153c/omt
Rv2689c/-	(cc=0.453)	info on Rv2689c/-
Rv0442c/PPE10	(cc=0.4458)	info on Rv0442c/PPE10
Rv1001/arcA	(cc=0.4333)	info on Rv1001/arcA
Rv0030/-	(cc=0.4276)	info on Rv0030/-
Rv0958/-	(cc=0.4067)	info on Rv0958/-
Rv2756c/hsdM	(cc=0.3986)	info on Rv2756c/hsdM
Rv0591/mce2C	(cc=0.3969)	info on Rv0591/mce2C
Rv0698/-	(cc=0.3943)	info on Rv0698/-
Rv2407/-	(cc=0.3892)	info on Rv2407/-

Correlation of Rv0590/mce2B with Rv2689c/-

Normalized LFCs for Rv0590/mce2B:
(description and provenance of datasets)

	Rv0590/mce2B	Rv2689c/-
Fe_supp_jason_reseq	-2.234	-1.129
low_pH_jason_reseq	0.918	-1.012
NO_jason_reseq	0.614	0.559
B6_jason_reseq	-2.589	-0.512
MHCII_jason_reseq	-1.251	-1.4
Isoniazid02	0.713	-1.215
Rifampicin4	-0.791	0.357
Ethambutol3	-0.422	0.664
Meropenem3	-0.399	-0.204
Vancomycin16	-0.6	0.263
Rv2680_day32	-0.828	-0.353
H37Rv_KO_MarP	-0.175	-0.014
hypoxia_3wks	-0.586	-0.59
hypoxia_6wks	-0.361	-0.019
glycerol	-0.193	0.69
cholesterol	0.073	0.132
AJ	0.203	0.274
Bibs02	1.084	-0.154
Bibs02c	-0.859	-0.811
BL6	-0.614	0.373
BL6a	-0.399	-0.151
BXD01	0.05	0.596
BXD010	0.128	0.713
BXD011	-0.236	1.253
BXD03	-0.054	0.133
BXD04	0.047	-0.028
BXD05	0.984	0.696
BXD06	-0.473	0.54
BXD07	-0.152	0.818
BXD08	-0.447	0.427
BXD09	-0.095	0.525
CAST	0.23	0.662
CCcont	-0.04	0.308
DS01	-0.294	-0.335
DS02	0.164	-0.049
DS04	0.682	0.978
DS0c	0.217	-1.273
GP01	-0.425	0.084
GP02	0.052	0.453
GP0c	0.68	0.366
NOD	0.853	0.236
NZO	-0.402	0.756
PWK	0.148	1.159
H37Rv_KO_CtpC	0.379	0.856
H37Rv_KO_CtpD	0.796	-0.387
H37Rv_KO_Rv1272	0.106	0.203
H37Rv_KO_SugABC	1.642	0.59
H37Rv_KO_MbtN	-1.093	-0.164
Trans05	-1.339	0.084
macrophage_unactivated	0.133	0.104
IL1	-0.756	-0.021
Rapamycin	0.252	-0.424
Tcell	0.137	0.371
GMCSF	-0.478	-0.726
IFNab	0.308	-0.245
IFNg	0.166	-0.735
IFNg_GMCSF1	0.848	-0.669
Rv1432_day32	1.043	0.188
Rv1565c_day32	-0.607	-0.194
secA2_input	-0.398	0.626
delta_Rv3594	-0.791	-0.171
delta_Rv3717	-0.715	0.518
delta_Rv3811	0.378	0.018
delta_Rv0954	-1.314	-0.229
PonA1	-2.641	-0.774
EccD1_KO	0.72	0.441
EspI_KO	1.121	0.844
PE35_KO	-0.064	0.233
PPE68_KO	0.819	0.464
glycerol2	0.038	0.593
lignocerate	0.911	0.928
oleate	0.112	0.373
phosphatidylcholine	0.562	0.723
acetate	1.16	1.082
glucAc	0.931	0.601
Rv0950ko	0.525	-0.16
Rv1096ko	0.323	-0.712
Rv3684ko	-0.187	0.783
delta_otsA_trehalose	2.804	2.741