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 Rv1621c/cydD:

update plot	correlation	link to info on gene
Rv1623c/cydA	(cc=0.8676)	info on Rv1623c/cydA
Rv1622c/cydB	(cc=0.8409)	info on Rv1622c/cydB
Rv1620c/cydC	(cc=0.6593)	info on Rv1620c/cydC
Rv2190c/-	(cc=0.4788)	info on Rv2190c/-
Rv2553c/-	(cc=0.459)	info on Rv2553c/-
Rv1836c/-	(cc=0.4588)	info on Rv1836c/-
Rv3102c/ftsE	(cc=0.4566)	info on Rv3102c/ftsE
Rv3207c/-	(cc=0.4486)	info on Rv3207c/-
Rv0950c/-	(cc=0.4478)	info on Rv0950c/-
Rv2144c/-	(cc=0.4276)	info on Rv2144c/-

Correlation of Rv1621c/cydD with Rv1622c/cydB

Normalized LFCs for Rv1621c/cydD:
(description and provenance of datasets)

	Rv1621c/cydD	Rv1622c/cydB
Fe_supp_jason_reseq	2.816	0.218
low_pH_jason_reseq	0.592	0.811
NO_jason_reseq	-1.864	-1.63
B6_jason_reseq	-0.941	-1.11
MHCII_jason_reseq	-0.829	-0.977
Isoniazid02	0.0	0.0
Rifampicin4	0.0	0.0
Ethambutol3	0.0	0.0
Meropenem3	0.0	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	2.016	0.584
H37Rv_KO_MarP	-1.861	-1.576
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.0	0.0
cholesterol	0.0	0.398
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.209	0.0
BL6	0.0	0.125
BL6a	0.973	0.696
BXD01	0.248	0.358
BXD010	0.352	0.859
BXD011	0.923	1.05
BXD03	0.831	0.135
BXD04	0.124	0.0
BXD05	0.256	0.135
BXD06	0.254	0.566
BXD07	0.138	0.138
BXD08	0.467	0.253
BXD09	0.78	0.386
CAST	0.0	0.0
CCcont	1.231	1.606
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.37	0.194
DS0c	0.0	0.0
GP01	2.631	3.382
GP02	1.891	2.044
GP0c	3.759	3.233
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	1.556	0.901
H37Rv_KO_CtpD	1.991	0.445
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.189	0.099
H37Rv_KO_MbtN	4.932	4.101
Trans05	0.0	0.0
macrophage_unactivated	0.0	0.83
IL1	3.921	2.011
Rapamycin	0.0	0.807
Tcell	0.0	0.0
GMCSF	1.545	0.694
IFNab	0.0	0.417
IFNg	1.109	0.369
IFNg_GMCSF1	1.581	0.434
Rv1432_day32	1.106	3.687
Rv1565c_day32	1.579	0.766
secA2_input	0.131	0.0
delta_Rv3594	0.0	0.34
delta_Rv3717	1.443	1.472
delta_Rv3811	0.0	-0.187
delta_Rv0954	1.862	0.416
PonA1	2.86	1.154
EccD1_KO	-0.559	-0.635
EspI_KO	0.827	-0.55
PE35_KO	-0.767	-0.271
PPE68_KO	0.25	0.0
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.0
glucAc	0.143	0.0
Rv0950ko	-3.278	-2.723
Rv1096ko	-1.396	-1.022
Rv3684ko	0.924	1.163
delta_otsA_trehalose	-2.12	-2.127