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 Rv1711/-:

update plot	correlation	link to info on gene
Rv0811c/-	(cc=0.6035)	info on Rv0811c/-
Rv2548A/-	(cc=0.5225)	info on Rv2548A/-
Rv3741c/-	(cc=0.5046)	info on Rv3741c/-
Rv0589/mce2A	(cc=0.4985)	info on Rv0589/mce2A
Rv2581c/-	(cc=0.4905)	info on Rv2581c/-
Rv3905c/esxF	(cc=0.4859)	info on Rv3905c/esxF
Rv2195/qcrA	(cc=0.4838)	info on Rv2195/qcrA
Rv2880c/-	(cc=0.4759)	info on Rv2880c/-
Rv3748/-	(cc=0.4688)	info on Rv3748/-
Rv0990c/-	(cc=0.4576)	info on Rv0990c/-

Correlation of Rv1711/- with Rv0990c/-

Normalized LFCs for Rv1711/-:
(description and provenance of datasets)

	Rv1711/-	Rv0990c/-
Fe_supp_jason_reseq	0.218	-1.389
low_pH_jason_reseq	0.0	0.683
NO_jason_reseq	0.0	-0.499
B6_jason_reseq	0.0	0.178
MHCII_jason_reseq	0.0	0.942
Isoniazid02	0.0	-0.138
Rifampicin4	0.374	-0.455
Ethambutol3	0.461	0.315
Meropenem3	0.0	0.359
Vancomycin16	0.0	-0.066
Rv2680_day32	0.0	-0.444
H37Rv_KO_MarP	0.195	-0.179
hypoxia_3wks	0.0	-0.514
hypoxia_6wks	0.0	-0.963
glycerol	0.0	0.19
cholesterol	0.0	-0.302
AJ	0.0	0.459
Bibs02	0.0	-0.261
Bibs02c	0.0	-0.605
BL6	0.0	0.157
BL6a	0.0	0.082
BXD01	0.0	-0.413
BXD010	0.0	0.199
BXD011	0.0	0.476
BXD03	0.0	-0.204
BXD04	0.0	-0.837
BXD05	0.0	-0.757
BXD06	0.0	-0.475
BXD07	0.0	-0.338
BXD08	0.0	-0.312
BXD09	0.0	-0.472
CAST	0.0	-0.582
CCcont	0.0	-0.312
DS01	0.0	0.311
DS02	0.0	0.624
DS04	0.0	0.514
DS0c	0.0	0.679
GP01	0.0	0.16
GP02	0.0	0.23
GP0c	0.0	0.479
NOD	0.0	0.225
NZO	0.0	1.087
PWK	0.0	0.014
H37Rv_KO_CtpC	0.0	0.244
H37Rv_KO_CtpD	0.0	0.22
H37Rv_KO_Rv1272	0.0	-0.271
H37Rv_KO_SugABC	0.0	0.403
H37Rv_KO_MbtN	0.103	0.579
Trans05	0.0	0.947
macrophage_unactivated	0.0	0.06
IL1	0.0	0.762
Rapamycin	0.0	0.737
Tcell	0.0	-0.714
GMCSF	0.0	-0.293
IFNab	0.0	0.284
IFNg	0.0	0.102
IFNg_GMCSF1	0.0	-0.06
Rv1432_day32	0.0	-0.227
Rv1565c_day32	0.0	-0.066
secA2_input	-0.593	-0.285
delta_Rv3594	-0.635	-1.386
delta_Rv3717	-1.114	-1.475
delta_Rv3811	-0.501	-2.195
delta_Rv0954	-1.632	-0.282
PonA1	-0.898	-0.136
EccD1_KO	0.414	1.901
EspI_KO	1.791	2.935
PE35_KO	0.0	0.974
PPE68_KO	0.0	1.312
glycerol2	0.0	-1.819
lignocerate	0.0	-0.437
oleate	0.0	-0.486
phosphatidylcholine	0.0	-0.916
acetate	0.0	0.06
glucAc	0.0	-0.716
Rv0950ko	0.416	-0.223
Rv1096ko	0.793	-0.362
Rv3684ko	0.452	0.452
delta_otsA_trehalose	-0.122	-0.111