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 Rv3487c/lipF:

update plot	correlation	link to info on gene
Rv3425/PPE57	(cc=0.5702)	info on Rv3425/PPE57
Rv0072/-	(cc=0.5657)	info on Rv0072/-
Rv3840/-	(cc=0.552)	info on Rv3840/-
Rv2443/dctA	(cc=0.5494)	info on Rv2443/dctA
Rv1386/PE15	(cc=0.5433)	info on Rv1386/PE15
Rv3784/-	(cc=0.5374)	info on Rv3784/-
Rv1509/-	(cc=0.5351)	info on Rv1509/-
Rv1831/-	(cc=0.5211)	info on Rv1831/-
Rv1787/PPE25	(cc=0.5186)	info on Rv1787/PPE25
Rv2430c/PPE41	(cc=0.5167)	info on Rv2430c/PPE41

Correlation of Rv3487c/lipF with Rv3784/-

Normalized LFCs for Rv3487c/lipF:
(description and provenance of datasets)

	Rv3487c/lipF	Rv3784/-
Fe_supp_jason_reseq	-0.019	0.006
low_pH_jason_reseq	-1.251	-0.898
NO_jason_reseq	-0.239	-0.21
B6_jason_reseq	-0.625	0.092
MHCII_jason_reseq	-0.39	0.297
Isoniazid02	0.253	0.688
Rifampicin4	0.084	-0.138
Ethambutol3	0.445	1.0
Meropenem3	-0.216	0.948
Vancomycin16	-0.151	0.066
Rv2680_day32	-0.366	0.337
H37Rv_KO_MarP	0.374	0.03
hypoxia_3wks	0.072	-0.04
hypoxia_6wks	0.58	0.092
glycerol	-0.127	0.522
cholesterol	-0.321	0.186
AJ	0.242	0.546
Bibs02	0.181	0.0
Bibs02c	-0.299	0.588
BL6	0.189	0.22
BL6a	0.083	0.455
BXD01	0.158	0.05
BXD010	0.391	0.168
BXD011	0.364	0.112
BXD03	0.223	-0.091
BXD04	0.761	0.291
BXD05	0.801	-0.244
BXD06	0.025	0.22
BXD07	0.311	-0.032
BXD08	0.615	0.132
BXD09	0.034	0.236
CAST	0.457	0.506
CCcont	0.187	0.043
DS01	0.031	0.185
DS02	-0.447	0.495
DS04	0.777	-0.07
DS0c	-0.676	0.176
GP01	0.17	0.273
GP02	1.009	0.114
GP0c	-0.039	-0.022
NOD	0.703	1.71
NZO	-0.143	0.363
PWK	0.595	0.482
H37Rv_KO_CtpC	0.674	0.437
H37Rv_KO_CtpD	0.353	0.656
H37Rv_KO_Rv1272	0.153	0.346
H37Rv_KO_SugABC	0.648	0.607
H37Rv_KO_MbtN	0.375	0.892
Trans05	0.556	0.842
macrophage_unactivated	0.256	0.413
IL1	-0.059	-0.51
Rapamycin	-0.031	0.077
Tcell	0.042	-0.222
GMCSF	-0.209	-0.235
IFNab	-0.082	-0.187
IFNg	0.462	0.094
IFNg_GMCSF1	0.163	0.248
Rv1432_day32	0.808	0.623
Rv1565c_day32	0.419	-0.316
secA2_input	0.122	-0.726
delta_Rv3594	-0.378	-0.494
delta_Rv3717	-0.602	-0.488
delta_Rv3811	-0.47	-0.175
delta_Rv0954	-0.77	-0.552
PonA1	-0.34	-0.545
EccD1_KO	-0.118	-0.135
EspI_KO	-0.262	0.225
PE35_KO	-1.105	-0.152
PPE68_KO	-0.752	-0.33
glycerol2	0.604	0.737
lignocerate	0.57	0.811
oleate	0.693	0.777
phosphatidylcholine	0.787	0.817
acetate	-0.274	0.243
glucAc	0.247	0.267
Rv0950ko	0.374	0.166
Rv1096ko	-0.543	-0.621
Rv3684ko	-1.123	-0.606
delta_otsA_trehalose	-0.799	-0.267