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 Rv1001/arcA:

update plot	correlation	link to info on gene
Rv2407/-	(cc=0.4887)	info on Rv2407/-
Rv1834/lipZ	(cc=0.4686)	info on Rv1834/lipZ
Rv0089/-	(cc=0.4683)	info on Rv0089/-
Rv1686c/-	(cc=0.4662)	info on Rv1686c/-
Rv0368c/-	(cc=0.4534)	info on Rv0368c/-
Rv1852/ureG	(cc=0.4527)	info on Rv1852/ureG
Rv0992c/-	(cc=0.4513)	info on Rv0992c/-
Rv1527c/pks5	(cc=0.4495)	info on Rv1527c/pks5
Rv1226c/-	(cc=0.4431)	info on Rv1226c/-
Rv2826c/-	(cc=0.442)	info on Rv2826c/-

Correlation of Rv1001/arcA with Rv1686c/-

Normalized LFCs for Rv1001/arcA:
(description and provenance of datasets)

	Rv1001/arcA	Rv1686c/-
Fe_supp_jason_reseq	-1.085	0.14
low_pH_jason_reseq	-0.228	-0.39
NO_jason_reseq	-0.638	0.079
B6_jason_reseq	-0.595	-1.537
MHCII_jason_reseq	-0.084	-0.948
Isoniazid02	-0.146	0.071
Rifampicin4	-0.347	0.133
Ethambutol3	-0.097	-0.094
Meropenem3	0.921	-0.518
Vancomycin16	0.329	0.066
Rv2680_day32	-0.112	-0.109
H37Rv_KO_MarP	0.152	-0.265
hypoxia_3wks	-0.215	-0.678
hypoxia_6wks	-0.418	-0.355
glycerol	0.348	1.175
cholesterol	-0.47	0.581
AJ	0.43	0.748
Bibs02	0.593	1.462
Bibs02c	0.011	-0.299
BL6	-0.266	0.319
BL6a	-0.362	-0.184
BXD01	-0.736	-1.233
BXD010	-0.364	-0.557
BXD011	-0.165	0.055
BXD03	-0.007	-0.588
BXD04	-0.098	-0.981
BXD05	-0.221	-1.133
BXD06	-0.461	-0.938
BXD07	-0.236	-0.557
BXD08	-0.608	-0.935
BXD09	-0.417	0.031
CAST	-0.058	0.924
CCcont	-0.194	0.158
DS01	0.315	0.152
DS02	0.2	-1.177
DS04	0.039	1.178
DS0c	-0.207	-0.423
GP01	0.493	1.264
GP02	-0.142	1.076
GP0c	0.247	0.852
NOD	-0.493	0.281
NZO	0.04	-0.045
PWK	0.593	0.207
H37Rv_KO_CtpC	-0.451	-0.453
H37Rv_KO_CtpD	-0.121	0.134
H37Rv_KO_Rv1272	-0.158	-0.166
H37Rv_KO_SugABC	0.89	0.832
H37Rv_KO_MbtN	0.205	0.459
Trans05	0.728	0.028
macrophage_unactivated	-0.581	-0.928
IL1	0.19	-0.113
Rapamycin	0.175	0.0
Tcell	0.134	0.358
GMCSF	0.066	0.38
IFNab	-0.23	-0.236
IFNg	-0.492	0.0
IFNg_GMCSF1	0.374	0.666
Rv1432_day32	1.235	1.284
Rv1565c_day32	-0.025	0.044
secA2_input	0.277	-1.218
delta_Rv3594	0.153	-0.046
delta_Rv3717	-0.122	0.073
delta_Rv3811	-0.028	-0.489
delta_Rv0954	0.43	0.216
PonA1	-0.591	0.28
EccD1_KO	0.0	-0.286
EspI_KO	0.605	-0.607
PE35_KO	0.248	-0.254
PPE68_KO	0.605	-1.481
glycerol2	-0.053	0.0
lignocerate	0.459	0.505
oleate	0.0	-0.829
phosphatidylcholine	-0.204	0.253
acetate	1.042	1.026
glucAc	0.706	1.882
Rv0950ko	0.516	0.268
Rv1096ko	0.467	0.685
Rv3684ko	0.426	-0.206
delta_otsA_trehalose	1.169	2.277