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 Rv2770c/PPE44

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

	Rv1959c/parE1	Rv2770c/PPE44
Fe_supp_jason_reseq	0.009	-0.586
low_pH_jason_reseq	-1.134	-0.698
NO_jason_reseq	-0.336	-0.231
B6_jason_reseq	-0.642	-0.296
MHCII_jason_reseq	0.022	-0.062
Isoniazid02	0.399	1.358
Rifampicin4	0.19	0.011
Ethambutol3	0.034	0.537
Meropenem3	0.541	0.046
Vancomycin16	0.239	0.194
Rv2680_day32	-0.014	0.04
H37Rv_KO_MarP	-0.464	0.119
hypoxia_3wks	-0.243	0.427
hypoxia_6wks	0.182	0.069
glycerol	-0.218	-0.372
cholesterol	-0.259	-0.456
AJ	0.422	0.469
Bibs02	-0.34	0.038
Bibs02c	-1.125	0.289
BL6	0.0	-0.362
BL6a	-0.903	0.211
BXD01	-0.148	0.072
BXD010	0.426	-0.009
BXD011	-0.317	0.54
BXD03	-0.74	0.354
BXD04	-0.165	-0.302
BXD05	-0.395	0.064
BXD06	-0.507	-0.152
BXD07	-0.23	-0.107
BXD08	-0.833	0.189
BXD09	-0.556	0.138
CAST	0.496	0.063
CCcont	-0.405	-0.604
DS01	0.291	0.14
DS02	-0.375	-0.088
DS04	-0.16	1.072
DS0c	0.025	0.599
GP01	0.558	0.85
GP02	0.867	1.191
GP0c	0.261	0.263
NOD	1.516	0.41
NZO	0.1	0.087
PWK	-0.236	0.377
H37Rv_KO_CtpC	0.357	0.639
H37Rv_KO_CtpD	0.273	0.533
H37Rv_KO_Rv1272	-0.467	0.521
H37Rv_KO_SugABC	-0.706	-0.04
H37Rv_KO_MbtN	1.447	0.178
Trans05	0.244	0.178
macrophage_unactivated	-1.136	0.347
IL1	1.086	0.151
Rapamycin	0.758	0.485
Tcell	-0.616	0.492
GMCSF	0.982	0.301
IFNab	1.073	0.435
IFNg	0.184	0.508
IFNg_GMCSF1	1.266	1.163
Rv1432_day32	0.018	-0.083
Rv1565c_day32	-0.689	-0.325
secA2_input	-1.398	-0.092
delta_Rv3594	-0.02	0.734
delta_Rv3717	0.298	0.327
delta_Rv3811	0.207	0.314
delta_Rv0954	0.601	0.367
PonA1	-0.98	0.382
EccD1_KO	0.546	-0.421
EspI_KO	0.405	0.234
PE35_KO	0.607	-0.239
PPE68_KO	-0.528	-0.278
glycerol2	0.801	0.71
lignocerate	0.196	0.464
oleate	1.144	1.138
phosphatidylcholine	4.052	0.945
acetate	-0.469	-0.492
glucAc	-0.748	-0.525
Rv0950ko	-0.57	0.374
Rv1096ko	-0.458	-0.398
Rv3684ko	-0.265	-0.092
delta_otsA_trehalose	1.713	-0.162