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 Rv2479c/-:

update plot	correlation	link to info on gene
Rv2814c/-	(cc=0.9867)	info on Rv2814c/-
Rv3185/-	(cc=0.9805)	info on Rv3185/-
Rv2167c/-	(cc=0.9764)	info on Rv2167c/-
Rv1756c/-	(cc=0.976)	info on Rv1756c/-
Rv2106/-	(cc=0.9716)	info on Rv2106/-
Rv3326/-	(cc=0.971)	info on Rv3326/-
Rv1369c/-	(cc=0.9707)	info on Rv1369c/-
Rv1764/-	(cc=0.968)	info on Rv1764/-
Rv2279/-	(cc=0.9617)	info on Rv2279/-
Rv2649/-	(cc=0.9609)	info on Rv2649/-

Correlation of Rv2479c/- with Rv3185/-

Normalized LFCs for Rv2479c/-:
(description and provenance of datasets)

	Rv2479c/-	Rv3185/-
Fe_supp_jason_reseq	-0.535	-0.396
low_pH_jason_reseq	-0.529	-0.432
NO_jason_reseq	-0.15	0.207
B6_jason_reseq	-0.465	-0.498
MHCII_jason_reseq	-0.222	-0.26
Isoniazid02	-0.09	-0.119
Rifampicin4	0.782	0.739
Ethambutol3	0.507	0.497
Meropenem3	-0.24	-0.314
Vancomycin16	-0.196	-0.149
Rv2680_day32	0.27	0.228
H37Rv_KO_MarP	-0.188	-0.181
hypoxia_3wks	0.459	0.407
hypoxia_6wks	0.063	-0.031
glycerol	-0.543	-0.55
cholesterol	0.151	0.215
AJ	1.467	1.345
Bibs02	1.211	1.221
Bibs02c	1.878	1.764
BL6	0.362	0.186
BL6a	1.179	1.099
BXD01	0.748	0.698
BXD010	1.05	0.919
BXD011	0.984	0.813
BXD03	0.814	0.71
BXD04	0.671	0.429
BXD05	1.219	1.003
BXD06	0.659	0.515
BXD07	0.867	0.846
BXD08	0.595	0.547
BXD09	0.812	0.723
CAST	1.51	1.343
CCcont	0.356	0.173
DS01	1.237	0.84
DS02	1.123	0.904
DS04	1.37	1.047
DS0c	1.292	1.006
GP01	1.356	1.126
GP02	1.464	1.316
GP0c	0.962	0.624
NOD	1.572	1.212
NZO	1.269	1.033
PWK	1.468	1.232
H37Rv_KO_CtpC	1.011	0.841
H37Rv_KO_CtpD	0.925	0.825
H37Rv_KO_Rv1272	0.739	0.538
H37Rv_KO_SugABC	0.917	0.903
H37Rv_KO_MbtN	0.659	0.658
Trans05	1.013	0.855
macrophage_unactivated	-0.814	-1.095
IL1	-0.765	-0.561
Rapamycin	-1.132	-0.534
Tcell	-1.714	-1.466
GMCSF	-0.581	-0.499
IFNab	-1.04	-0.998
IFNg	-0.711	-0.524
IFNg_GMCSF1	-0.355	-0.456
Rv1432_day32	0.378	0.462
Rv1565c_day32	0.145	0.15
secA2_input	0.18	0.25
delta_Rv3594	0.093	-0.067
delta_Rv3717	-0.034	-0.055
delta_Rv3811	0.0	-0.079
delta_Rv0954	0.553	0.494
PonA1	-0.021	0.03
EccD1_KO	0.151	-0.049
EspI_KO	0.799	0.901
PE35_KO	0.796	0.604
PPE68_KO	0.557	0.4
glycerol2	-0.733	-0.673
lignocerate	-0.438	-0.458
oleate	-0.829	-0.963
phosphatidylcholine	-0.648	-0.686
acetate	0.035	0.17
glucAc	0.179	0.022
Rv0950ko	0.081	-0.286
Rv1096ko	0.081	0.29
Rv3684ko	-0.596	-0.701
delta_otsA_trehalose	0.083	0.2