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 Rv1954A/-:

update plot	correlation	link to info on gene
Rv1954c/-	(cc=0.6871)	info on Rv1954c/-
Rv2040c/-	(cc=0.5504)	info on Rv2040c/-
Rv2562/-	(cc=0.5253)	info on Rv2562/-
Rv3166c/-	(cc=0.5018)	info on Rv3166c/-
Rv1088/PE9	(cc=0.4774)	info on Rv1088/PE9
Rv1580c/-	(cc=0.4723)	info on Rv1580c/-
Rv1561/vapC11	(cc=0.4606)	info on Rv1561/vapC11
Rv1508A/-	(cc=0.4324)	info on Rv1508A/-
Rv1583c/-	(cc=0.4282)	info on Rv1583c/-
Rv2481c/-	(cc=0.4281)	info on Rv2481c/-

Correlation of Rv1954A/- with Rv2481c/-

Normalized LFCs for Rv1954A/-:
(description and provenance of datasets)

	Rv1954A/-	Rv2481c/-
Fe_supp_jason_reseq	-0.051	0.434
low_pH_jason_reseq	-0.878	-0.092
NO_jason_reseq	0.795	-0.593
B6_jason_reseq	-1.023	-0.233
MHCII_jason_reseq	-0.98	-0.51
Isoniazid02	0.162	0.351
Rifampicin4	0.699	0.024
Ethambutol3	-0.047	0.214
Meropenem3	0.236	0.055
Vancomycin16	0.034	0.703
Rv2680_day32	0.267	0.682
H37Rv_KO_MarP	0.679	-0.497
hypoxia_3wks	-0.909	0.08
hypoxia_6wks	-1.04	0.921
glycerol	-1.412	0.159
cholesterol	-1.382	0.442
AJ	-0.906	0.321
Bibs02	-0.631	-1.599
Bibs02c	-0.423	0.573
BL6	1.662	1.853
BL6a	0.082	1.821
BXD01	-0.17	0.866
BXD010	0.235	1.509
BXD011	0.376	1.004
BXD03	1.021	1.65
BXD04	0.345	0.4
BXD05	1.009	1.885
BXD06	0.464	1.123
BXD07	0.734	1.091
BXD08	0.663	1.263
BXD09	0.683	1.301
CAST	-0.352	0.659
CCcont	-0.105	1.896
DS01	-0.441	-0.161
DS02	-0.199	0.663
DS04	0.049	-1.81
DS0c	-0.137	0.347
GP01	-0.69	0.995
GP02	0.515	1.273
GP0c	-0.193	0.217
NOD	-0.351	0.407
NZO	-1.113	-0.049
PWK	-0.756	0.804
H37Rv_KO_CtpC	-0.545	0.701
H37Rv_KO_CtpD	-0.004	-1.316
H37Rv_KO_Rv1272	1.449	1.848
H37Rv_KO_SugABC	-2.115	-1.683
H37Rv_KO_MbtN	-1.266	0.09
Trans05	0.628	1.478
macrophage_unactivated	-0.174	0.445
IL1	-0.065	0.478
Rapamycin	0.7	0.359
Tcell	0.414	0.342
GMCSF	0.121	0.19
IFNab	0.78	0.366
IFNg	0.123	0.182
IFNg_GMCSF1	1.084	0.201
Rv1432_day32	0.746	0.013
Rv1565c_day32	-0.839	-0.142
secA2_input	-1.506	-0.509
delta_Rv3594	0.021	0.031
delta_Rv3717	0.461	-1.226
delta_Rv3811	-0.32	-0.415
delta_Rv0954	-0.605	-0.849
PonA1	-0.433	-0.911
EccD1_KO	0.135	0.635
EspI_KO	0.713	0.508
PE35_KO	0.12	0.691
PPE68_KO	0.32	0.781
glycerol2	-0.046	1.184
lignocerate	0.557	1.4
oleate	-0.437	0.388
phosphatidylcholine	0.246	1.066
acetate	0.256	0.894
glucAc	0.797	0.948
Rv0950ko	-0.326	0.434
Rv1096ko	-0.745	-0.163
Rv3684ko	-1.896	0.252
delta_otsA_trehalose	-1.174	0.873