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 Rv1959c/parE1:

update plot	correlation	link to info on gene
Rv1770/-	(cc=0.4749)	info on Rv1770/-
Rv1863c/-	(cc=0.4098)	info on Rv1863c/-
Rv2143/-	(cc=0.4081)	info on Rv2143/-
Rv2770c/PPE44	(cc=0.4074)	info on Rv2770c/PPE44
Rv1882c/-	(cc=0.4025)	info on Rv1882c/-
Rv1668c/-	(cc=0.3991)	info on Rv1668c/-
Rv1871c/-	(cc=0.3959)	info on Rv1871c/-
Rv1074c/fadA3	(cc=0.3943)	info on Rv1074c/fadA3
Rv3121/cyp141	(cc=0.3925)	info on Rv3121/cyp141
Rv2972c/-	(cc=0.3913)	info on Rv2972c/-

Correlation of Rv1959c/parE1 with Rv1770/-

Normalized LFCs for Rv1959c/parE1:
(description and provenance of datasets)

	Rv1959c/parE1	Rv1770/-
Fe_supp_jason_reseq	0.009	-0.305
low_pH_jason_reseq	-1.134	-0.639
NO_jason_reseq	-0.336	-0.129
B6_jason_reseq	-0.642	-0.312
MHCII_jason_reseq	0.022	-0.042
Isoniazid02	0.399	0.346
Rifampicin4	0.19	0.693
Ethambutol3	0.034	0.153
Meropenem3	0.541	-0.35
Vancomycin16	0.239	0.348
Rv2680_day32	-0.014	-0.366
H37Rv_KO_MarP	-0.464	0.185
hypoxia_3wks	-0.243	0.124
hypoxia_6wks	0.182	-0.177
glycerol	-0.218	1.24
cholesterol	-0.259	0.39
AJ	0.422	0.612
Bibs02	-0.34	0.211
Bibs02c	-1.125	-0.579
BL6	0.0	0.312
BL6a	-0.903	0.075
BXD01	-0.148	0.252
BXD010	0.426	0.19
BXD011	-0.317	0.005
BXD03	-0.74	-0.052
BXD04	-0.165	0.108
BXD05	-0.395	-0.163
BXD06	-0.507	0.258
BXD07	-0.23	0.238
BXD08	-0.833	0.475
BXD09	-0.556	0.152
CAST	0.496	0.395
CCcont	-0.405	0.039
DS01	0.291	0.0
DS02	-0.375	0.025
DS04	-0.16	0.382
DS0c	0.025	-0.207
GP01	0.558	0.902
GP02	0.867	1.576
GP0c	0.261	0.72
NOD	1.516	0.228
NZO	0.1	-0.465
PWK	-0.236	-0.03
H37Rv_KO_CtpC	0.357	0.371
H37Rv_KO_CtpD	0.273	0.414
H37Rv_KO_Rv1272	-0.467	0.326
H37Rv_KO_SugABC	-0.706	-1.318
H37Rv_KO_MbtN	1.447	0.441
Trans05	0.244	0.944
macrophage_unactivated	-1.136	0.092
IL1	1.086	0.478
Rapamycin	0.758	0.927
Tcell	-0.616	0.287
GMCSF	0.982	0.615
IFNab	1.073	0.384
IFNg	0.184	0.604
IFNg_GMCSF1	1.266	0.459
Rv1432_day32	0.018	0.081
Rv1565c_day32	-0.689	0.25
secA2_input	-1.398	0.7
delta_Rv3594	-0.02	-0.497
delta_Rv3717	0.298	-0.39
delta_Rv3811	0.207	-0.751
delta_Rv0954	0.601	-0.235
PonA1	-0.98	-1.109
EccD1_KO	0.546	0.151
EspI_KO	0.405	0.131
PE35_KO	0.607	-0.015
PPE68_KO	-0.528	-0.067
glycerol2	0.801	0.738
lignocerate	0.196	0.475
oleate	1.144	1.0
phosphatidylcholine	4.052	0.815
acetate	-0.469	-0.288
glucAc	-0.748	-0.466
Rv0950ko	-0.57	0.229
Rv1096ko	-0.458	-0.793
Rv3684ko	-0.265	-0.337
delta_otsA_trehalose	1.713	1.702