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 Rv2429/ahpD:

update plot	correlation	link to info on gene
Rv0713/-	(cc=0.5404)	info on Rv0713/-
Rv1511/gmdA	(cc=0.4924)	info on Rv1511/gmdA
Rv2289/cdh	(cc=0.4917)	info on Rv2289/cdh
Rv2953/-	(cc=0.4832)	info on Rv2953/-
Rv0873/fadE10	(cc=0.4783)	info on Rv0873/fadE10
Rv2954c/-	(cc=0.4693)	info on Rv2954c/-
Rv2399c/cysT	(cc=0.4632)	info on Rv2399c/cysT
Rv3680/-	(cc=0.4458)	info on Rv3680/-
Rv3490/otsA	(cc=0.443)	info on Rv3490/otsA
Rv2284/lipM	(cc=0.4402)	info on Rv2284/lipM

Correlation of Rv2429/ahpD with Rv0873/fadE10

Normalized LFCs for Rv2429/ahpD:
(description and provenance of datasets)

	Rv2429/ahpD	Rv0873/fadE10
Fe_supp_jason_reseq	0.174	0.892
low_pH_jason_reseq	-0.867	-1.044
NO_jason_reseq	0.0	-0.732
B6_jason_reseq	0.363	0.425
MHCII_jason_reseq	1.557	0.675
Isoniazid02	-4.061	-0.908
Rifampicin4	0.171	0.341
Ethambutol3	0.32	-0.111
Meropenem3	-0.819	-0.593
Vancomycin16	0.167	-0.525
Rv2680_day32	-0.016	0.514
H37Rv_KO_MarP	0.567	0.306
hypoxia_3wks	0.311	-0.251
hypoxia_6wks	0.464	0.186
glycerol	0.178	0.184
cholesterol	0.015	0.542
AJ	0.513	-0.178
Bibs02	0.212	-0.282
Bibs02c	1.36	0.673
BL6	0.58	0.014
BL6a	1.118	0.485
BXD01	0.56	0.187
BXD010	-0.448	-0.229
BXD011	-0.123	-0.084
BXD03	0.107	-0.209
BXD04	0.418	0.271
BXD05	0.719	0.411
BXD06	0.053	0.055
BXD07	0.822	0.113
BXD08	0.04	0.251
BXD09	-0.044	-0.015
CAST	-0.072	-0.34
CCcont	0.816	-0.065
DS01	0.0	0.394
DS02	0.534	0.487
DS04	-0.37	0.08
DS0c	0.718	0.448
GP01	0.509	0.584
GP02	-1.258	1.007
GP0c	-1.082	0.131
NOD	0.57	-0.387
NZO	-0.481	0.123
PWK	0.155	-0.185
H37Rv_KO_CtpC	-0.592	-0.342
H37Rv_KO_CtpD	0.751	0.489
H37Rv_KO_Rv1272	0.029	0.61
H37Rv_KO_SugABC	0.283	0.11
H37Rv_KO_MbtN	0.401	0.058
Trans05	1.134	-0.131
macrophage_unactivated	0.294	0.253
IL1	-1.006	-0.374
Rapamycin	0.083	-0.285
Tcell	-0.228	0.072
GMCSF	1.014	0.341
IFNab	-0.085	-0.209
IFNg	0.732	0.139
IFNg_GMCSF1	0.17	-0.396
Rv1432_day32	0.9	0.175
Rv1565c_day32	0.147	-0.708
secA2_input	-2.016	-0.131
delta_Rv3594	1.462	0.459
delta_Rv3717	0.132	0.0
delta_Rv3811	1.077	0.446
delta_Rv0954	1.145	0.377
PonA1	0.709	0.521
EccD1_KO	-0.756	0.28
EspI_KO	0.171	0.67
PE35_KO	0.502	0.137
PPE68_KO	0.963	0.0
glycerol2	0.943	0.46
lignocerate	0.839	0.201
oleate	0.818	0.6
phosphatidylcholine	0.796	0.51
acetate	0.519	-0.298
glucAc	0.423	-0.621
Rv0950ko	-0.853	0.021
Rv1096ko	-1.668	-0.486
Rv3684ko	-1.723	-0.501
delta_otsA_trehalose	1.015	0.97