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 Rv0713/-

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

	Rv2429/ahpD	Rv0713/-
Fe_supp_jason_reseq	0.174	1.217
low_pH_jason_reseq	-0.867	-0.4
NO_jason_reseq	0.0	-0.223
B6_jason_reseq	0.363	0.443
MHCII_jason_reseq	1.557	1.131
Isoniazid02	-4.061	-1.464
Rifampicin4	0.171	0.146
Ethambutol3	0.32	-0.872
Meropenem3	-0.819	-1.261
Vancomycin16	0.167	-0.204
Rv2680_day32	-0.016	-0.5
H37Rv_KO_MarP	0.567	0.491
hypoxia_3wks	0.311	0.367
hypoxia_6wks	0.464	0.355
glycerol	0.178	-0.781
cholesterol	0.015	-0.668
AJ	0.513	-0.203
Bibs02	0.212	-0.191
Bibs02c	1.36	-0.149
BL6	0.58	-0.166
BL6a	1.118	-0.228
BXD01	0.56	0.261
BXD010	-0.448	0.199
BXD011	-0.123	-0.271
BXD03	0.107	-0.077
BXD04	0.418	0.179
BXD05	0.719	0.188
BXD06	0.053	0.225
BXD07	0.822	-0.264
BXD08	0.04	0.496
BXD09	-0.044	-0.211
CAST	-0.072	-0.527
CCcont	0.816	0.171
DS01	0.0	-0.494
DS02	0.534	-0.273
DS04	-0.37	-0.467
DS0c	0.718	-0.405
GP01	0.509	-0.61
GP02	-1.258	-1.011
GP0c	-1.082	-1.142
NOD	0.57	-0.386
NZO	-0.481	-1.05
PWK	0.155	0.148
H37Rv_KO_CtpC	-0.592	-0.585
H37Rv_KO_CtpD	0.751	0.152
H37Rv_KO_Rv1272	0.029	-0.472
H37Rv_KO_SugABC	0.283	0.26
H37Rv_KO_MbtN	0.401	0.537
Trans05	1.134	0.346
macrophage_unactivated	0.294	0.249
IL1	-1.006	-0.567
Rapamycin	0.083	-0.832
Tcell	-0.228	-0.466
GMCSF	1.014	0.066
IFNab	-0.085	-0.475
IFNg	0.732	-0.615
IFNg_GMCSF1	0.17	-0.899
Rv1432_day32	0.9	-0.72
Rv1565c_day32	0.147	-0.158
secA2_input	-2.016	-0.495
delta_Rv3594	1.462	0.081
delta_Rv3717	0.132	-0.063
delta_Rv3811	1.077	0.171
delta_Rv0954	1.145	-0.191
PonA1	0.709	-0.063
EccD1_KO	-0.756	0.306
EspI_KO	0.171	0.533
PE35_KO	0.502	0.123
PPE68_KO	0.963	0.134
glycerol2	0.943	0.751
lignocerate	0.839	0.581
oleate	0.818	0.784
phosphatidylcholine	0.796	0.829
acetate	0.519	-0.248
glucAc	0.423	-0.525
Rv0950ko	-0.853	-0.163
Rv1096ko	-1.668	-0.377
Rv3684ko	-1.723	-0.652
delta_otsA_trehalose	1.015	1.203