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 Rv1703c/-:

update plot	correlation	link to info on gene
Rv3322c/-	(cc=0.4862)	info on Rv3322c/-
Rv3749c/-	(cc=0.4839)	info on Rv3749c/-
Rv1356c/-	(cc=0.4417)	info on Rv1356c/-
Rv3407/vapB47	(cc=0.4409)	info on Rv3407/vapB47
Rv2253/-	(cc=0.4393)	info on Rv2253/-
Rv3697c/vapC48	(cc=0.4335)	info on Rv3697c/vapC48
Rv2287/yjcE	(cc=0.4193)	info on Rv2287/yjcE
Rv0182c/sigG	(cc=0.4169)	info on Rv0182c/sigG
Rv1531/-	(cc=0.4109)	info on Rv1531/-
Rv2424c/-	(cc=0.4089)	info on Rv2424c/-

Correlation of Rv1703c/- with Rv1356c/-

Normalized LFCs for Rv1703c/-:
(description and provenance of datasets)

	Rv1703c/-	Rv1356c/-
Fe_supp_jason_reseq	0.107	0.805
low_pH_jason_reseq	-0.709	-0.214
NO_jason_reseq	0.381	-0.478
B6_jason_reseq	0.215	0.18
MHCII_jason_reseq	0.726	0.023
Isoniazid02	0.179	1.425
Rifampicin4	0.046	0.217
Ethambutol3	0.143	1.228
Meropenem3	0.689	0.12
Vancomycin16	0.093	0.414
Rv2680_day32	-0.843	-0.561
H37Rv_KO_MarP	-0.161	-0.047
hypoxia_3wks	-0.048	0.291
hypoxia_6wks	-0.357	0.299
glycerol	-0.556	-0.705
cholesterol	0.183	-0.077
AJ	0.496	-0.187
Bibs02	0.51	-0.024
Bibs02c	-0.064	0.182
BL6	0.876	-0.066
BL6a	0.092	0.352
BXD01	0.342	-0.087
BXD010	0.054	-0.158
BXD011	-0.051	0.111
BXD03	0.085	-0.547
BXD04	0.0	0.298
BXD05	0.154	-0.47
BXD06	0.017	-0.107
BXD07	-0.151	-0.56
BXD08	0.163	-0.243
BXD09	0.024	0.171
CAST	0.41	0.0
CCcont	0.503	-0.418
DS01	0.262	-0.125
DS02	0.232	-0.236
DS04	-0.059	0.814
DS0c	0.778	0.289
GP01	0.301	0.689
GP02	0.234	1.014
GP0c	0.645	0.0
NOD	0.317	0.696
NZO	0.811	0.026
PWK	-0.196	0.026
H37Rv_KO_CtpC	-0.162	0.271
H37Rv_KO_CtpD	0.923	0.225
H37Rv_KO_Rv1272	0.317	0.555
H37Rv_KO_SugABC	0.276	1.183
H37Rv_KO_MbtN	-0.85	-1.266
Trans05	0.841	1.178
macrophage_unactivated	0.129	1.048
IL1	-0.448	-3.601
Rapamycin	-0.911	-2.704
Tcell	0.769	4.259
GMCSF	-0.745	-3.057
IFNab	-0.357	-2.875
IFNg	-0.112	-2.061
IFNg_GMCSF1	-1.024	-1.741
Rv1432_day32	1.047	-0.172
Rv1565c_day32	0.731	-1.717
secA2_input	-0.249	-0.7
delta_Rv3594	-0.295	0.323
delta_Rv3717	-0.701	-0.107
delta_Rv3811	-0.498	0.586
delta_Rv0954	-0.536	0.509
PonA1	0.119	0.159
EccD1_KO	-0.069	0.704
EspI_KO	0.733	0.841
PE35_KO	0.718	0.624
PPE68_KO	0.787	0.685
glycerol2	0.476	-0.024
lignocerate	0.554	0.1
oleate	0.352	0.184
phosphatidylcholine	0.665	0.246
acetate	-0.236	0.028
glucAc	-0.196	-0.289
Rv0950ko	0.395	-0.042
Rv1096ko	-0.283	-0.721
Rv3684ko	0.445	-0.783
delta_otsA_trehalose	-0.066	0.814