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 Rv1527c/pks5

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

	Rv1001/arcA	Rv1527c/pks5
Fe_supp_jason_reseq	-1.085	0.175
low_pH_jason_reseq	-0.228	-0.587
NO_jason_reseq	-0.638	-0.155
B6_jason_reseq	-0.595	0.181
MHCII_jason_reseq	-0.084	0.229
Isoniazid02	-0.146	-0.015
Rifampicin4	-0.347	-0.057
Ethambutol3	-0.097	0.225
Meropenem3	0.921	0.915
Vancomycin16	0.329	-0.056
Rv2680_day32	-0.112	-0.199
H37Rv_KO_MarP	0.152	0.189
hypoxia_3wks	-0.215	0.159
hypoxia_6wks	-0.418	0.294
glycerol	0.348	0.196
cholesterol	-0.47	0.013
AJ	0.43	0.622
Bibs02	0.593	0.15
Bibs02c	0.011	0.477
BL6	-0.266	0.251
BL6a	-0.362	0.066
BXD01	-0.736	-0.215
BXD010	-0.364	0.021
BXD011	-0.165	-0.262
BXD03	-0.007	-0.108
BXD04	-0.098	-0.508
BXD05	-0.221	0.022
BXD06	-0.461	-0.39
BXD07	-0.236	-0.036
BXD08	-0.608	0.022
BXD09	-0.417	-0.304
CAST	-0.058	-0.12
CCcont	-0.194	0.025
DS01	0.315	0.554
DS02	0.2	0.126
DS04	0.039	0.455
DS0c	-0.207	0.325
GP01	0.493	1.712
GP02	-0.142	0.477
GP0c	0.247	0.555
NOD	-0.493	0.304
NZO	0.04	0.314
PWK	0.593	-0.017
H37Rv_KO_CtpC	-0.451	0.314
H37Rv_KO_CtpD	-0.121	0.143
H37Rv_KO_Rv1272	-0.158	0.415
H37Rv_KO_SugABC	0.89	0.611
H37Rv_KO_MbtN	0.205	-0.13
Trans05	0.728	0.289
macrophage_unactivated	-0.581	-0.158
IL1	0.19	-0.074
Rapamycin	0.175	-0.114
Tcell	0.134	-0.081
GMCSF	0.066	0.19
IFNab	-0.23	-0.151
IFNg	-0.492	-0.134
IFNg_GMCSF1	0.374	0.189
Rv1432_day32	1.235	0.216
Rv1565c_day32	-0.025	-0.104
secA2_input	0.277	0.523
delta_Rv3594	0.153	0.021
delta_Rv3717	-0.122	-0.374
delta_Rv3811	-0.028	0.312
delta_Rv0954	0.43	-0.172
PonA1	-0.591	0.492
EccD1_KO	0.0	0.089
EspI_KO	0.605	0.262
PE35_KO	0.248	0.23
PPE68_KO	0.605	0.378
glycerol2	-0.053	0.46
lignocerate	0.459	0.673
oleate	0.0	0.373
phosphatidylcholine	-0.204	0.696
acetate	1.042	0.845
glucAc	0.706	0.441
Rv0950ko	0.516	0.422
Rv1096ko	0.467	0.311
Rv3684ko	0.426	0.498
delta_otsA_trehalose	1.169	0.551