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 Rv2833c/ugpB:

update plot	correlation	link to info on gene
Rv2481c/-	(cc=0.6002)	info on Rv2481c/-
Rv2456c/-	(cc=0.5803)	info on Rv2456c/-
Rv2562/-	(cc=0.5305)	info on Rv2562/-
Rv0188/-	(cc=0.5302)	info on Rv0188/-
Rv0844c/narL	(cc=0.5279)	info on Rv0844c/narL
Rv0463/-	(cc=0.5193)	info on Rv0463/-
Rv1471/trxB1	(cc=0.5189)	info on Rv1471/trxB1
Rv0055/rpsR1	(cc=0.5066)	info on Rv0055/rpsR1
Rv1076/lipU	(cc=0.5061)	info on Rv1076/lipU
Rv0944/-	(cc=0.4935)	info on Rv0944/-

Correlation of Rv2833c/ugpB with Rv2481c/-

Normalized LFCs for Rv2833c/ugpB:
(description and provenance of datasets)

	Rv2833c/ugpB	Rv2481c/-
Fe_supp_jason_reseq	-1.047	0.434
low_pH_jason_reseq	-0.855	-0.092
NO_jason_reseq	-0.496	-0.593
B6_jason_reseq	-2.495	-0.233
MHCII_jason_reseq	-1.705	-0.51
Isoniazid02	0.323	0.351
Rifampicin4	1.283	0.024
Ethambutol3	0.505	0.214
Meropenem3	0.497	0.055
Vancomycin16	0.939	0.703
Rv2680_day32	1.035	0.682
H37Rv_KO_MarP	-0.188	-0.497
hypoxia_3wks	0.0	0.08
hypoxia_6wks	-0.234	0.921
glycerol	-0.693	0.159
cholesterol	0.552	0.442
AJ	-0.541	0.321
Bibs02	-0.736	-1.599
Bibs02c	-1.429	0.573
BL6	1.972	1.853
BL6a	1.025	1.821
BXD01	0.8	0.866
BXD010	1.237	1.509
BXD011	0.812	1.004
BXD03	1.088	1.65
BXD04	0.67	0.4
BXD05	0.391	1.885
BXD06	0.91	1.123
BXD07	1.167	1.091
BXD08	1.509	1.263
BXD09	1.334	1.301
CAST	2.478	0.659
CCcont	1.651	1.896
DS01	-0.551	-0.161
DS02	0.699	0.663
DS04	-0.905	-1.81
DS0c	-0.506	0.347
GP01	-0.086	0.995
GP02	-0.568	1.273
GP0c	-0.237	0.217
NOD	0.0	0.407
NZO	0.309	-0.049
PWK	-0.915	0.804
H37Rv_KO_CtpC	1.177	0.701
H37Rv_KO_CtpD	-1.086	-1.316
H37Rv_KO_Rv1272	1.385	1.848
H37Rv_KO_SugABC	-0.949	-1.683
H37Rv_KO_MbtN	-0.625	0.09
Trans05	1.851	1.478
macrophage_unactivated	0.65	0.445
IL1	0.392	0.478
Rapamycin	0.921	0.359
Tcell	0.903	0.342
GMCSF	0.731	0.19
IFNab	0.163	0.366
IFNg	0.216	0.182
IFNg_GMCSF1	0.17	0.201
Rv1432_day32	-0.961	0.013
Rv1565c_day32	-0.24	-0.142
secA2_input	0.095	-0.509
delta_Rv3594	-0.402	0.031
delta_Rv3717	-0.802	-1.226
delta_Rv3811	-0.651	-0.415
delta_Rv0954	-0.45	-0.849
PonA1	-0.799	-0.911
EccD1_KO	-1.47	0.635
EspI_KO	0.091	0.508
PE35_KO	0.443	0.691
PPE68_KO	0.202	0.781
glycerol2	0.873	1.184
lignocerate	1.376	1.4
oleate	0.489	0.388
phosphatidylcholine	1.108	1.066
acetate	1.079	0.894
glucAc	1.205	0.948
Rv0950ko	0.582	0.434
Rv1096ko	0.995	-0.163
Rv3684ko	1.588	0.252
delta_otsA_trehalose	-1.327	0.873