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 Rv1854c/ndh:

update plot	correlation	link to info on gene
Rv0973c/accA2	(cc=0.5649)	info on Rv0973c/accA2
Rv2842c/-	(cc=0.5435)	info on Rv2842c/-
Rv2374c/hrcA	(cc=0.5417)	info on Rv2374c/hrcA
Rv1116/-	(cc=0.54)	info on Rv1116/-
Rv1925/fadD31	(cc=0.5306)	info on Rv1925/fadD31
Rv0055/rpsR1	(cc=0.5223)	info on Rv0055/rpsR1
Rv2243/fabD	(cc=0.5181)	info on Rv2243/fabD
Rv3361c/-	(cc=0.5137)	info on Rv3361c/-
Rv3152/nuoH	(cc=0.5104)	info on Rv3152/nuoH
Rv3112/moaD1	(cc=0.504)	info on Rv3112/moaD1

Correlation of Rv1854c/ndh with Rv3361c/-

Normalized LFCs for Rv1854c/ndh:
(description and provenance of datasets)

	Rv1854c/ndh	Rv3361c/-
Fe_supp_jason_reseq	0.0	-0.043
low_pH_jason_reseq	0.694	-1.718
NO_jason_reseq	-0.69	0.945
B6_jason_reseq	-0.292	-1.08
MHCII_jason_reseq	-0.257	-2.216
Isoniazid02	0.551	-0.146
Rifampicin4	0.0	-0.872
Ethambutol3	0.0	-0.544
Meropenem3	0.454	-0.535
Vancomycin16	0.0	-0.546
Rv2680_day32	0.0	0.249
H37Rv_KO_MarP	0.371	0.6
hypoxia_3wks	0.0	-0.072
hypoxia_6wks	0.464	0.355
glycerol	0.0	1.837
cholesterol	0.0	-0.381
AJ	0.0	-0.138
Bibs02	0.183	-0.775
Bibs02c	0.0	1.801
BL6	2.702	2.544
BL6a	1.633	2.527
BXD01	1.985	2.895
BXD010	2.767	2.856
BXD011	2.116	1.935
BXD03	0.75	0.722
BXD04	1.656	1.346
BXD05	0.135	0.935
BXD06	1.934	2.714
BXD07	0.851	1.965
BXD08	3.214	3.001
BXD09	1.998	2.618
CAST	0.0	0.791
CCcont	0.733	2.308
DS01	0.0	1.42
DS02	0.0	0.35
DS04	0.0	-0.51
DS0c	0.0	0.0
GP01	0.0	-0.418
GP02	0.0	0.694
GP0c	0.0	0.0
NOD	0.0	3.83
NZO	0.0	-0.678
PWK	0.0	-1.009
H37Rv_KO_CtpC	3.466	1.224
H37Rv_KO_CtpD	0.0	-0.651
H37Rv_KO_Rv1272	2.343	2.571
H37Rv_KO_SugABC	0.0	-0.122
H37Rv_KO_MbtN	0.506	2.626
Trans05	1.305	0.742
macrophage_unactivated	-1.051	1.411
IL1	1.293	0.715
Rapamycin	0.129	0.988
Tcell	0.267	1.3
GMCSF	-1.172	0.562
IFNab	-0.547	0.81
IFNg	0.815	0.93
IFNg_GMCSF1	-1.046	0.101
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	-1.052
secA2_input	1.634	1.781
delta_Rv3594	0.211	3.105
delta_Rv3717	1.165	0.927
delta_Rv3811	0.0	2.235
delta_Rv0954	0.0	2.421
PonA1	0.0	0.931
EccD1_KO	0.793	-0.22
EspI_KO	1.275	0.841
PE35_KO	0.368	1.015
PPE68_KO	0.403	2.4
glycerol2	0.0	0.0
lignocerate	0.168	0.0
oleate	0.0	0.746
phosphatidylcholine	0.0	0.499
acetate	0.437	-0.658
glucAc	0.501	-0.666
Rv0950ko	-1.894	-0.229
Rv1096ko	-1.167	-0.597
Rv3684ko	1.428	1.172
delta_otsA_trehalose	-0.468	-1.407