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 Rv1623c/cydA:

update plot	correlation	link to info on gene
Rv1621c/cydD	(cc=0.8676)	info on Rv1621c/cydD
Rv1622c/cydB	(cc=0.8667)	info on Rv1622c/cydB
Rv1620c/cydC	(cc=0.7071)	info on Rv1620c/cydC
Rv2190c/-	(cc=0.6095)	info on Rv2190c/-
Rv3207c/-	(cc=0.5483)	info on Rv3207c/-
Rv1836c/-	(cc=0.5086)	info on Rv1836c/-
Rv2696c/-	(cc=0.4776)	info on Rv2696c/-
Rv1507A/-	(cc=0.4725)	info on Rv1507A/-
Rv1551/plsB1	(cc=0.4678)	info on Rv1551/plsB1
Rv2144c/-	(cc=0.4666)	info on Rv2144c/-

Correlation of Rv1623c/cydA with Rv1621c/cydD

Normalized LFCs for Rv1623c/cydA:
(description and provenance of datasets)

	Rv1623c/cydA	Rv1621c/cydD
Fe_supp_jason_reseq	2.363	2.816
low_pH_jason_reseq	1.506	0.592
NO_jason_reseq	-4.702	-1.864
B6_jason_reseq	-0.759	-0.941
MHCII_jason_reseq	-1.292	-0.829
Isoniazid02	-0.183	0.0
Rifampicin4	-0.341	0.0
Ethambutol3	0.0	0.0
Meropenem3	-0.151	0.0
Vancomycin16	-0.334	0.0
Rv2680_day32	0.728	2.016
H37Rv_KO_MarP	-2.253	-1.861
hypoxia_3wks	0.0	0.0
hypoxia_6wks	-0.464	0.0
glycerol	1.138	0.0
cholesterol	0.381	0.0
AJ	0.324	0.0
Bibs02	-0.642	0.0
Bibs02c	1.593	0.209
BL6	0.254	0.0
BL6a	2.593	0.973
BXD01	0.416	0.248
BXD010	0.88	0.352
BXD011	1.938	0.923
BXD03	0.875	0.831
BXD04	1.837	0.124
BXD05	1.118	0.256
BXD06	1.719	0.254
BXD07	1.555	0.138
BXD08	1.274	0.467
BXD09	1.542	0.78
CAST	-0.581	0.0
CCcont	2.556	1.231
DS01	-0.38	0.0
DS02	-0.764	0.0
DS04	0.916	0.37
DS0c	0.157	0.0
GP01	3.382	2.631
GP02	3.182	1.891
GP0c	4.011	3.759
NOD	-0.566	0.0
NZO	-0.503	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	1.865	1.556
H37Rv_KO_CtpD	0.405	1.991
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.37	0.189
H37Rv_KO_MbtN	5.071	4.932
Trans05	0.0	0.0
macrophage_unactivated	0.303	0.0
IL1	3.111	3.921
Rapamycin	0.571	0.0
Tcell	-0.166	0.0
GMCSF	2.297	1.545
IFNab	0.0	0.0
IFNg	1.694	1.109
IFNg_GMCSF1	0.584	1.581
Rv1432_day32	4.133	1.106
Rv1565c_day32	1.579	1.579
secA2_input	-1.082	0.131
delta_Rv3594	0.0	0.0
delta_Rv3717	1.664	1.443
delta_Rv3811	-0.348	0.0
delta_Rv0954	2.017	1.862
PonA1	3.713	2.86
EccD1_KO	-0.286	-0.559
EspI_KO	0.77	0.827
PE35_KO	-1.467	-0.767
PPE68_KO	0.634	0.25
glycerol2	0.14	0.0
lignocerate	0.235	0.0
oleate	0.0	0.0
phosphatidylcholine	0.14	0.0
acetate	0.603	0.0
glucAc	0.74	0.143
Rv0950ko	-3.986	-3.278
Rv1096ko	-1.24	-1.396
Rv3684ko	0.986	0.924
delta_otsA_trehalose	-2.142	-2.12