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 Rv1620c/cydC:

update plot	correlation	link to info on gene
Rv1623c/cydA	(cc=0.7071)	info on Rv1623c/cydA
Rv1622c/cydB	(cc=0.6724)	info on Rv1622c/cydB
Rv1621c/cydD	(cc=0.6593)	info on Rv1621c/cydD
Rv1551/plsB1	(cc=0.4214)	info on Rv1551/plsB1
Rv2439c/proB	(cc=0.4143)	info on Rv2439c/proB
Rv1159/pimE	(cc=0.4127)	info on Rv1159/pimE
Rv3207c/-	(cc=0.4073)	info on Rv3207c/-
Rv0127/mak	(cc=0.4043)	info on Rv0127/mak
Rv1867/-	(cc=0.4019)	info on Rv1867/-
Rv0412c/-	(cc=0.3948)	info on Rv0412c/-

Correlation of Rv1620c/cydC with Rv1621c/cydD

Normalized LFCs for Rv1620c/cydC:
(description and provenance of datasets)

	Rv1620c/cydC	Rv1621c/cydD
Fe_supp_jason_reseq	0.398	2.816
low_pH_jason_reseq	-0.811	0.592
NO_jason_reseq	-2.809	-1.864
B6_jason_reseq	-1.187	-0.941
MHCII_jason_reseq	-1.046	-0.829
Isoniazid02	-0.383	0.0
Rifampicin4	0.0	0.0
Ethambutol3	-0.32	0.0
Meropenem3	-0.315	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	0.764	2.016
H37Rv_KO_MarP	-2.145	-1.861
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.471	0.0
cholesterol	-0.132	0.0
AJ	-0.212	0.0
Bibs02	-0.167	0.0
Bibs02c	-0.399	0.209
BL6	0.376	0.0
BL6a	0.319	0.973
BXD01	-0.119	0.248
BXD010	0.206	0.352
BXD011	0.464	0.923
BXD03	-0.258	0.831
BXD04	2.242	0.124
BXD05	1.505	0.256
BXD06	0.641	0.254
BXD07	-0.126	0.138
BXD08	0.485	0.467
BXD09	0.226	0.78
CAST	0.0	0.0
CCcont	1.016	1.231
DS01	-0.45	0.0
DS02	-0.414	0.0
DS04	-0.37	0.37
DS0c	-0.198	0.0
GP01	3.117	2.631
GP02	4.755	1.891
GP0c	3.61	3.759
NOD	-0.428	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.135	1.556
H37Rv_KO_CtpD	0.381	1.991
H37Rv_KO_Rv1272	-0.269	0.0
H37Rv_KO_SugABC	-0.09	0.189
H37Rv_KO_MbtN	2.607	4.932
Trans05	-0.249	0.0
macrophage_unactivated	0.761	0.0
IL1	1.326	3.921
Rapamycin	0.74	0.0
Tcell	0.0	0.0
GMCSF	-0.364	1.545
IFNab	0.0	0.0
IFNg	0.93	1.109
IFNg_GMCSF1	0.757	1.581
Rv1432_day32	0.999	1.106
Rv1565c_day32	0.599	1.579
secA2_input	0.477	0.131
delta_Rv3594	0.164	0.0
delta_Rv3717	1.114	1.443
delta_Rv3811	-0.358	0.0
delta_Rv0954	0.894	1.862
PonA1	3.025	2.86
EccD1_KO	0.352	-0.559
EspI_KO	2.165	0.827
PE35_KO	0.601	-0.767
PPE68_KO	0.96	0.25
glycerol2	0.531	0.0
lignocerate	0.712	0.0
oleate	0.0	0.0
phosphatidylcholine	0.193	0.0
acetate	1.127	0.0
glucAc	1.306	0.143
Rv0950ko	-1.616	-3.278
Rv1096ko	0.148	-1.396
Rv3684ko	3.435	0.924
delta_otsA_trehalose	0.226	-2.12