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 Rv1221/sigE:

update plot	correlation	link to info on gene
Rv1514c/-	(cc=0.5759)	info on Rv1514c/-
Rv1388/mihF	(cc=0.533)	info on Rv1388/mihF
Rv2359/zur	(cc=0.5326)	info on Rv2359/zur
Rv0910/-	(cc=0.5261)	info on Rv0910/-
Rv1473/-	(cc=0.5212)	info on Rv1473/-
Rv1631/coaE	(cc=0.4953)	info on Rv1631/coaE
Rv0634c/-	(cc=0.4945)	info on Rv0634c/-
Rv3603c/-	(cc=0.491)	info on Rv3603c/-
Rv1182/papA3	(cc=0.489)	info on Rv1182/papA3
Rv3827c/-	(cc=0.4885)	info on Rv3827c/-

Correlation of Rv1221/sigE with Rv1631/coaE

Normalized LFCs for Rv1221/sigE:
(description and provenance of datasets)

	Rv1221/sigE	Rv1631/coaE
Fe_supp_jason_reseq	2.602	1.07
low_pH_jason_reseq	0.156	0.0
NO_jason_reseq	0.895	0.0
B6_jason_reseq	0.752	0.0
MHCII_jason_reseq	1.311	0.0
Isoniazid02	0.682	1.548
Rifampicin4	0.146	0.341
Ethambutol3	-0.646	-0.168
Meropenem3	-0.212	-0.165
Vancomycin16	-0.305	-0.366
Rv2680_day32	0.651	0.0
H37Rv_KO_MarP	-0.313	-0.313
hypoxia_3wks	-0.128	0.0
hypoxia_6wks	-1.495	0.0
glycerol	-0.967	0.0
cholesterol	-0.197	0.0
AJ	-0.373	0.0
Bibs02	-0.698	0.0
Bibs02c	-0.39	0.0
BL6	-1.107	0.0
BL6a	-0.472	0.0
BXD01	-0.58	0.0
BXD010	-0.749	0.0
BXD011	-1.333	0.0
BXD03	-0.79	0.0
BXD04	-1.035	0.0
BXD05	0.33	0.0
BXD06	-0.832	0.0
BXD07	-1.713	0.0
BXD08	-1.392	0.0
BXD09	-0.374	0.0
CAST	-1.927	0.0
CCcont	-0.397	0.41
DS01	0.286	0.0
DS02	-0.35	0.0
DS04	-0.929	0.0
DS0c	-0.193	0.0
GP01	-1.292	0.0
GP02	-0.92	0.0
GP0c	-1.702	0.0
NOD	-1.487	0.0
NZO	-1.669	0.0
PWK	-1.147	0.0
H37Rv_KO_CtpC	-1.359	0.0
H37Rv_KO_CtpD	-0.113	0.0
H37Rv_KO_Rv1272	-1.846	0.0
H37Rv_KO_SugABC	-1.159	0.099
H37Rv_KO_MbtN	-0.459	0.0
Trans05	0.23	0.0
macrophage_unactivated	0.202	0.0
IL1	-0.629	0.0
Rapamycin	-0.424	0.0
Tcell	-1.212	0.0
GMCSF	-0.269	0.0
IFNab	-0.641	0.0
IFNg	-0.994	0.0
IFNg_GMCSF1	-2.049	0.0
Rv1432_day32	-0.139	0.0
Rv1565c_day32	0.158	0.0
secA2_input	-0.931	-0.47
delta_Rv3594	0.057	0.402
delta_Rv3717	-0.736	0.0
delta_Rv3811	-0.171	0.391
delta_Rv0954	-0.149	0.178
PonA1	1.154	2.389
EccD1_KO	-0.28	0.0
EspI_KO	1.383	0.328
PE35_KO	2.856	0.335
PPE68_KO	2.003	1.03
glycerol2	0.42	0.0
lignocerate	-0.647	0.0
oleate	0.457	0.0
phosphatidylcholine	0.513	0.0
acetate	-0.949	0.0
glucAc	-1.283	0.0
Rv0950ko	-1.643	-0.302
Rv1096ko	-1.644	-1.348
Rv3684ko	-2.05	0.0
delta_otsA_trehalose	0.322	0.254