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 Rv3425/PPE57

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

	Rv3487c/lipF	Rv3425/PPE57
Fe_supp_jason_reseq	-0.019	0.598
low_pH_jason_reseq	-1.251	-0.669
NO_jason_reseq	-0.239	-0.488
B6_jason_reseq	-0.625	-0.79
MHCII_jason_reseq	-0.39	-0.124
Isoniazid02	0.253	-0.224
Rifampicin4	0.084	0.206
Ethambutol3	0.445	0.092
Meropenem3	-0.216	-0.096
Vancomycin16	-0.151	0.05
Rv2680_day32	-0.366	-0.384
H37Rv_KO_MarP	0.374	1.099
hypoxia_3wks	0.072	0.215
hypoxia_6wks	0.58	0.451
glycerol	-0.127	0.404
cholesterol	-0.321	-0.369
AJ	0.242	0.429
Bibs02	0.181	-0.775
Bibs02c	-0.299	0.856
BL6	0.189	0.421
BL6a	0.083	1.065
BXD01	0.158	0.637
BXD010	0.391	0.822
BXD011	0.364	0.4
BXD03	0.223	0.746
BXD04	0.761	0.642
BXD05	0.801	1.02
BXD06	0.025	0.444
BXD07	0.311	0.916
BXD08	0.615	0.604
BXD09	0.034	0.845
CAST	0.457	0.389
CCcont	0.187	0.365
DS01	0.031	0.623
DS02	-0.447	0.013
DS04	0.777	-0.16
DS0c	-0.676	0.366
GP01	0.17	0.413
GP02	1.009	0.959
GP0c	-0.039	0.689
NOD	0.703	0.146
NZO	-0.143	1.144
PWK	0.595	-0.269
H37Rv_KO_CtpC	0.674	0.59
H37Rv_KO_CtpD	0.353	0.139
H37Rv_KO_Rv1272	0.153	0.317
H37Rv_KO_SugABC	0.648	0.247
H37Rv_KO_MbtN	0.375	0.396
Trans05	0.556	0.463
macrophage_unactivated	0.256	0.502
IL1	-0.059	0.122
Rapamycin	-0.031	0.19
Tcell	0.042	0.499
GMCSF	-0.209	-0.288
IFNab	-0.082	0.042
IFNg	0.462	0.791
IFNg_GMCSF1	0.163	0.949
Rv1432_day32	0.808	0.233
Rv1565c_day32	0.419	-0.531
secA2_input	0.122	-0.454
delta_Rv3594	-0.378	-0.069
delta_Rv3717	-0.602	-1.0
delta_Rv3811	-0.47	0.033
delta_Rv0954	-0.77	0.181
PonA1	-0.34	0.208
EccD1_KO	-0.118	-0.743
EspI_KO	-0.262	-0.607
PE35_KO	-1.105	-1.199
PPE68_KO	-0.752	-0.602
glycerol2	0.604	0.395
lignocerate	0.57	0.619
oleate	0.693	0.624
phosphatidylcholine	0.787	0.829
acetate	-0.274	0.078
glucAc	0.247	0.095
Rv0950ko	0.374	-0.208
Rv1096ko	-0.543	-1.161
Rv3684ko	-1.123	-0.737
delta_otsA_trehalose	-0.799	-0.32