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 Rv3422c/-:

update plot	correlation	link to info on gene
Rv2730/-	(cc=0.5022)	info on Rv2730/-
Rv2160c/-	(cc=0.4971)	info on Rv2160c/-
Rv3419c/gcp	(cc=0.4935)	info on Rv3419c/gcp
Rv2993c/-	(cc=0.4915)	info on Rv2993c/-
Rv2818c/-	(cc=0.4868)	info on Rv2818c/-
Rv2530c/vapC39	(cc=0.4772)	info on Rv2530c/vapC39
Rv1239c/corA	(cc=0.4488)	info on Rv1239c/corA
Rv3133c/devR	(cc=0.4477)	info on Rv3133c/devR
Rv1059/-	(cc=0.4408)	info on Rv1059/-
Rv1214c/PE14	(cc=0.4386)	info on Rv1214c/PE14

Correlation of Rv3422c/- with Rv2730/-

Normalized LFCs for Rv3422c/-:
(description and provenance of datasets)

	Rv3422c/-	Rv2730/-
Fe_supp_jason_reseq	-0.882	-0.497
low_pH_jason_reseq	0.673	-0.304
NO_jason_reseq	0.953	-0.113
B6_jason_reseq	-1.648	-1.853
MHCII_jason_reseq	-1.317	-0.93
Isoniazid02	-0.706	-0.499
Rifampicin4	-0.29	-0.514
Ethambutol3	0.0	0.636
Meropenem3	-0.417	-1.533
Vancomycin16	0.0	-1.011
Rv2680_day32	-0.131	1.433
H37Rv_KO_MarP	0.313	0.645
hypoxia_3wks	-1.388	-0.981
hypoxia_6wks	-1.013	-0.28
glycerol	0.385	0.38
cholesterol	0.0	0.392
AJ	2.318	0.287
Bibs02	0.0	0.592
Bibs02c	0.399	0.344
BL6	0.0	0.77
BL6a	0.839	0.997
BXD01	1.953	0.404
BXD010	1.856	0.517
BXD011	0.448	1.284
BXD03	2.509	0.797
BXD04	0.959	0.732
BXD05	1.497	1.264
BXD06	2.067	0.822
BXD07	2.857	1.492
BXD08	0.467	0.755
BXD09	0.943	0.843
CAST	0.0	0.434
CCcont	0.0	0.344
DS01	0.0	0.351
DS02	0.0	0.682
DS04	1.599	0.319
DS0c	0.0	0.68
GP01	0.347	0.536
GP02	0.0	0.106
GP0c	0.13	0.059
NOD	0.0	0.517
NZO	0.548	0.11
PWK	0.374	-0.213
H37Rv_KO_CtpC	0.309	1.034
H37Rv_KO_CtpD	3.385	0.063
H37Rv_KO_Rv1272	0.0	0.551
H37Rv_KO_SugABC	0.099	1.139
H37Rv_KO_MbtN	0.0	0.337
Trans05	0.0	1.448
macrophage_unactivated	0.338	-0.426
IL1	0.317	-0.077
Rapamycin	0.328	-0.872
Tcell	-0.375	-0.701
GMCSF	0.544	-0.016
IFNab	0.323	-0.375
IFNg	-0.644	-0.516
IFNg_GMCSF1	-0.361	-0.239
Rv1432_day32	0.0	1.087
Rv1565c_day32	0.0	-0.032
secA2_input	-0.316	-0.888
delta_Rv3594	0.532	0.823
delta_Rv3717	3.11	0.622
delta_Rv3811	1.282	0.773
delta_Rv0954	1.375	1.071
PonA1	3.481	0.855
EccD1_KO	0.664	-0.418
EspI_KO	1.081	0.22
PE35_KO	-0.683	0.015
PPE68_KO	0.646	0.189
glycerol2	-0.68	-1.013
lignocerate	-0.591	-0.51
oleate	-0.688	-1.165
phosphatidylcholine	-0.679	-0.311
acetate	-0.806	-0.249
glucAc	-0.501	-0.028
Rv0950ko	-0.832	0.651
Rv1096ko	-1.58	-0.118
Rv3684ko	0.757	-0.203
delta_otsA_trehalose	0.0	-0.107