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 Rv2998/-:

update plot	correlation	link to info on gene
Rv1508A/-	(cc=0.5325)	info on Rv1508A/-
Rv2492/-	(cc=0.5168)	info on Rv2492/-
Rv0691c/-	(cc=0.5138)	info on Rv0691c/-
Rv3138/pflA	(cc=0.5123)	info on Rv3138/pflA
Rv0567/-	(cc=0.4873)	info on Rv0567/-
Rv2310/-	(cc=0.4857)	info on Rv2310/-
Rv1269c/-	(cc=0.4854)	info on Rv1269c/-
Rv2880c/-	(cc=0.4774)	info on Rv2880c/-
Rv0934/pstS1	(cc=0.4497)	info on Rv0934/pstS1
Rv0557/mgtA	(cc=0.4462)	info on Rv0557/mgtA

Correlation of Rv2998/- with Rv2492/-

Normalized LFCs for Rv2998/-:
(description and provenance of datasets)

	Rv2998/-	Rv2492/-
Fe_supp_jason_reseq	0.0	1.025
low_pH_jason_reseq	-1.074	-0.134
NO_jason_reseq	0.378	-0.549
B6_jason_reseq	-0.74	0.605
MHCII_jason_reseq	0.621	0.244
Isoniazid02	-0.723	0.477
Rifampicin4	0.647	-0.347
Ethambutol3	-0.373	0.541
Meropenem3	-1.329	0.919
Vancomycin16	-0.568	-0.523
Rv2680_day32	-2.766	-0.883
H37Rv_KO_MarP	0.401	0.209
hypoxia_3wks	0.044	0.128
hypoxia_6wks	0.67	0.198
glycerol	-0.357	-0.228
cholesterol	-0.07	0.076
AJ	-0.015	1.044
Bibs02	-0.558	0.23
Bibs02c	0.571	-0.647
BL6	0.368	-0.387
BL6a	0.927	0.296
BXD01	0.66	0.164
BXD010	-0.018	-0.034
BXD011	0.008	1.053
BXD03	0.289	-0.153
BXD04	0.389	0.912
BXD05	1.214	0.321
BXD06	0.642	0.318
BXD07	0.769	0.498
BXD08	0.684	0.452
BXD09	0.576	0.305
CAST	0.137	0.449
CCcont	-0.389	-0.462
DS01	-0.536	0.063
DS02	-0.438	-0.12
DS04	-0.208	0.29
DS0c	1.571	0.471
GP01	1.334	0.373
GP02	-0.538	-0.498
GP0c	-0.23	0.694
NOD	-0.174	-0.539
NZO	-0.663	0.967
PWK	0.993	0.293
H37Rv_KO_CtpC	0.613	0.044
H37Rv_KO_CtpD	1.171	0.218
H37Rv_KO_Rv1272	0.714	0.944
H37Rv_KO_SugABC	-1.841	-0.99
H37Rv_KO_MbtN	-1.256	0.482
Trans05	0.127	0.0
macrophage_unactivated	0.877	-0.234
IL1	0.068	0.504
Rapamycin	0.071	-0.227
Tcell	0.345	-0.365
GMCSF	1.085	0.364
IFNab	0.121	0.0
IFNg	0.535	0.096
IFNg_GMCSF1	0.214	-1.012
Rv1432_day32	1.7	1.197
Rv1565c_day32	-0.381	-0.047
secA2_input	-0.304	-0.836
delta_Rv3594	-2.168	-1.491
delta_Rv3717	-1.986	-1.165
delta_Rv3811	-1.698	-0.986
delta_Rv0954	-1.265	-1.018
PonA1	-2.401	-1.244
EccD1_KO	1.214	0.908
EspI_KO	0.633	0.106
PE35_KO	1.896	1.479
PPE68_KO	1.609	1.536
glycerol2	0.371	-0.147
lignocerate	-0.186	-0.537
oleate	0.74	0.33
phosphatidylcholine	0.577	-0.073
acetate	-0.977	-0.909
glucAc	-1.121	-1.29
Rv0950ko	0.757	-0.096
Rv1096ko	1.707	-1.348
Rv3684ko	-0.242	-0.216
delta_otsA_trehalose	-2.389	-0.487