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 Rv3689/-:

update plot	correlation	link to info on gene
Rv1072/-	(cc=0.6562)	info on Rv1072/-
Rv1387/PPE20	(cc=0.6534)	info on Rv1387/PPE20
Rv3694c/-	(cc=0.6327)	info on Rv3694c/-
Rv1386/PE15	(cc=0.62)	info on Rv1386/PE15
Rv3419c/gcp	(cc=0.6172)	info on Rv3419c/gcp
Rv1616/-	(cc=0.6155)	info on Rv1616/-
Rv3142c/-	(cc=0.5926)	info on Rv3142c/-
Rv0932c/pstS2	(cc=0.5862)	info on Rv0932c/pstS2
Rv1488/-	(cc=0.5853)	info on Rv1488/-
Rv2456c/-	(cc=0.5823)	info on Rv2456c/-

Correlation of Rv3689/- with Rv1072/-

Normalized LFCs for Rv3689/-:
(description and provenance of datasets)

	Rv3689/-	Rv1072/-
Fe_supp_jason_reseq	-0.388	3.452
low_pH_jason_reseq	-1.681	0.709
NO_jason_reseq	0.105	-0.205
B6_jason_reseq	0.499	1.58
MHCII_jason_reseq	-0.62	0.0
Isoniazid02	-1.107	-2.007
Rifampicin4	0.495	-0.653
Ethambutol3	0.951	3.263
Meropenem3	-0.364	0.586
Vancomycin16	-0.058	-0.727
Rv2680_day32	-0.811	-0.803
H37Rv_KO_MarP	-1.24	-2.718
hypoxia_3wks	0.638	0.0
hypoxia_6wks	0.739	1.451
glycerol	-0.295	0.089
cholesterol	-0.2	-1.261
AJ	0.576	0.948
Bibs02	-0.311	0.747
Bibs02c	-0.073	0.653
BL6	0.728	2.081
BL6a	0.844	1.728
BXD01	1.055	3.146
BXD010	0.8	2.277
BXD011	0.852	3.036
BXD03	1.454	2.899
BXD04	1.548	5.696
BXD05	1.047	2.5
BXD06	0.962	2.909
BXD07	1.026	2.518
BXD08	1.004	3.668
BXD09	0.486	1.736
CAST	1.677	4.513
CCcont	0.27	2.429
DS01	-0.202	0.965
DS02	0.044	0.821
DS04	0.225	0.793
DS0c	-0.091	0.748
GP01	0.821	0.0
GP02	0.096	-0.166
GP0c	0.85	-0.26
NOD	0.957	1.87
NZO	1.16	0.815
PWK	2.364	2.865
H37Rv_KO_CtpC	0.806	3.557
H37Rv_KO_CtpD	0.981	1.054
H37Rv_KO_Rv1272	0.967	1.837
H37Rv_KO_SugABC	1.067	1.948
H37Rv_KO_MbtN	1.472	2.179
Trans05	0.496	2.15
macrophage_unactivated	0.079	-1.13
IL1	-0.374	-1.949
Rapamycin	-0.997	-2.961
Tcell	0.508	1.466
GMCSF	0.132	-1.191
IFNab	0.206	0.0
IFNg	0.722	-1.756
IFNg_GMCSF1	0.452	-0.465
Rv1432_day32	1.172	-0.887
Rv1565c_day32	-0.482	0.401
secA2_input	-0.488	1.079
delta_Rv3594	-0.58	-0.846
delta_Rv3717	-0.205	-2.079
delta_Rv3811	-0.21	-0.717
delta_Rv0954	-0.979	-2.135
PonA1	-0.099	-1.272
EccD1_KO	0.122	1.312
EspI_KO	-0.217	1.041
PE35_KO	0.295	0.306
PPE68_KO	0.208	0.653
glycerol2	0.27	-0.451
lignocerate	-0.029	-0.897
oleate	0.717	-0.588
phosphatidylcholine	-0.052	-1.207
acetate	0.284	-0.535
glucAc	0.188	0.554
Rv0950ko	0.202	0.28
Rv1096ko	0.85	2.524
Rv3684ko	0.799	2.6
delta_otsA_trehalose	-0.482	-1.013