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 Rv2289/cdh

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

	Rv2429/ahpD	Rv2289/cdh
Fe_supp_jason_reseq	0.174	0.226
low_pH_jason_reseq	-0.867	-0.189
NO_jason_reseq	0.0	-0.885
B6_jason_reseq	0.363	-0.483
MHCII_jason_reseq	1.557	0.024
Isoniazid02	-4.061	-0.893
Rifampicin4	0.171	-0.406
Ethambutol3	0.32	0.979
Meropenem3	-0.819	-0.37
Vancomycin16	0.167	-0.615
Rv2680_day32	-0.016	-0.164
H37Rv_KO_MarP	0.567	0.065
hypoxia_3wks	0.311	0.0
hypoxia_6wks	0.464	-0.443
glycerol	0.178	0.29
cholesterol	0.015	0.374
AJ	0.513	0.751
Bibs02	0.212	0.563
Bibs02c	1.36	0.574
BL6	0.58	0.089
BL6a	1.118	0.453
BXD01	0.56	-0.151
BXD010	-0.448	0.443
BXD011	-0.123	0.314
BXD03	0.107	0.784
BXD04	0.418	0.071
BXD05	0.719	0.567
BXD06	0.053	0.374
BXD07	0.822	-0.094
BXD08	0.04	-0.03
BXD09	-0.044	0.486
CAST	-0.072	0.315
CCcont	0.816	0.385
DS01	0.0	0.231
DS02	0.534	-0.032
DS04	-0.37	-0.24
DS0c	0.718	0.0
GP01	0.509	1.094
GP02	-1.258	-0.931
GP0c	-1.082	0.019
NOD	0.57	-0.187
NZO	-0.481	0.311
PWK	0.155	-0.058
H37Rv_KO_CtpC	-0.592	0.419
H37Rv_KO_CtpD	0.751	0.954
H37Rv_KO_Rv1272	0.029	-0.085
H37Rv_KO_SugABC	0.283	0.97
H37Rv_KO_MbtN	0.401	0.897
Trans05	1.134	0.396
macrophage_unactivated	0.294	0.451
IL1	-1.006	0.303
Rapamycin	0.083	-0.055
Tcell	-0.228	-0.238
GMCSF	1.014	0.797
IFNab	-0.085	0.133
IFNg	0.732	0.273
IFNg_GMCSF1	0.17	0.295
Rv1432_day32	0.9	-0.022
Rv1565c_day32	0.147	0.019
secA2_input	-2.016	-1.431
delta_Rv3594	1.462	0.828
delta_Rv3717	0.132	0.466
delta_Rv3811	1.077	0.577
delta_Rv0954	1.145	-0.174
PonA1	0.709	0.25
EccD1_KO	-0.756	1.161
EspI_KO	0.171	0.841
PE35_KO	0.502	1.575
PPE68_KO	0.963	1.59
glycerol2	0.943	0.425
lignocerate	0.839	0.516
oleate	0.818	-0.142
phosphatidylcholine	0.796	0.13
acetate	0.519	0.437
glucAc	0.423	0.401
Rv0950ko	-0.853	0.039
Rv1096ko	-1.668	-0.751
Rv3684ko	-1.723	-0.688
delta_otsA_trehalose	1.015	0.333