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 Rv3165c/-:

update plot	correlation	link to info on gene
Rv2740/ephG	(cc=0.4995)	info on Rv2740/ephG
Rv0769/-	(cc=0.4668)	info on Rv0769/-
Rv0499/-	(cc=0.4548)	info on Rv0499/-
Rv1499/-	(cc=0.4524)	info on Rv1499/-
Rv2308/-	(cc=0.4365)	info on Rv2308/-
Rv2060/-	(cc=0.4245)	info on Rv2060/-
Rv1219c/-	(cc=0.4109)	info on Rv1219c/-
Rv3553/-	(cc=0.4092)	info on Rv3553/-
Rv1082/mca	(cc=0.4085)	info on Rv1082/mca
Rv2437/-	(cc=0.4063)	info on Rv2437/-

Correlation of Rv3165c/- with Rv2060/-

Normalized LFCs for Rv3165c/-:
(description and provenance of datasets)

	Rv3165c/-	Rv2060/-
Fe_supp_jason_reseq	1.427	-0.103
low_pH_jason_reseq	0.151	-1.673
NO_jason_reseq	-1.394	-0.601
B6_jason_reseq	0.333	-3.069
MHCII_jason_reseq	0.308	-0.784
Isoniazid02	-0.295	3.405
Rifampicin4	-0.309	0.969
Ethambutol3	-0.652	2.606
Meropenem3	0.024	0.289
Vancomycin16	0.027	-0.52
Rv2680_day32	2.941	0.249
H37Rv_KO_MarP	0.684	-0.471
hypoxia_3wks	-0.327	-1.894
hypoxia_6wks	-0.503	-0.393
glycerol	0.718	-1.549
cholesterol	-0.506	-0.229
AJ	0.128	-1.321
Bibs02	-0.603	-3.076
Bibs02c	-1.291	-0.182
BL6	-0.342	1.112
BL6a	0.161	1.633
BXD01	0.173	1.966
BXD010	1.189	1.646
BXD011	0.478	0.053
BXD03	0.706	0.455
BXD04	0.913	2.675
BXD05	-0.249	0.493
BXD06	0.829	2.147
BXD07	0.687	0.883
BXD08	0.143	2.281
BXD09	0.486	0.813
CAST	0.305	0.844
CCcont	0.661	2.499
DS01	-0.32	-1.916
DS02	-2.757	-1.238
DS04	-1.577	-2.311
DS0c	-0.715	-3.432
GP01	-0.715	-1.661
GP02	-1.448	-1.171
GP0c	-0.98	-0.446
NOD	-0.199	-0.838
NZO	0.564	-2.51
PWK	0.159	0.631
H37Rv_KO_CtpC	-0.567	-2.423
H37Rv_KO_CtpD	1.921	1.775
H37Rv_KO_Rv1272	-0.082	-0.484
H37Rv_KO_SugABC	-0.562	-1.666
H37Rv_KO_MbtN	0.877	-1.631
Trans05	1.323	1.218
macrophage_unactivated	1.266	3.671
IL1	1.023	1.619
Rapamycin	0.657	0.733
Tcell	0.896	3.874
GMCSF	1.766	-0.755
IFNab	0.686	0.493
IFNg	1.406	-1.16
IFNg_GMCSF1	0.0	-0.28
Rv1432_day32	-1.042	0.0
Rv1565c_day32	1.567	0.855
secA2_input	0.18	-1.227
delta_Rv3594	-0.529	1.146
delta_Rv3717	-0.062	2.154
delta_Rv3811	0.568	0.451
delta_Rv0954	-1.112	-0.549
PonA1	-1.602	-2.016
EccD1_KO	0.414	2.23
EspI_KO	1.198	1.266
PE35_KO	0.84	3.241
PPE68_KO	0.771	4.62
glycerol2	0.717	1.84
lignocerate	1.492	2.661
oleate	-3.549	-1.843
phosphatidylcholine	0.378	2.134
acetate	1.197	1.754
glucAc	1.646	1.848
Rv0950ko	0.265	3.784
Rv1096ko	0.09	2.494
Rv3684ko	-0.049	-0.314
delta_otsA_trehalose	0.111	0.818