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 Rv2431c/PE25:

update plot	correlation	link to info on gene
Rv0989c/grcC2	(cc=0.625)	info on Rv0989c/grcC2
Rv1504c/-	(cc=0.5577)	info on Rv1504c/-
Rv0073/-	(cc=0.5486)	info on Rv0073/-
Rv0832/PE_PGRS12	(cc=0.5339)	info on Rv0832/PE_PGRS12
Rv0456B/mazE1	(cc=0.5265)	info on Rv0456B/mazE1
Rv0820/phoT	(cc=0.526)	info on Rv0820/phoT
Rv2352c/PPE38	(cc=0.5239)	info on Rv2352c/PPE38
Rv2268c/cyp128	(cc=0.5114)	info on Rv2268c/cyp128
Rv3679/-	(cc=0.5094)	info on Rv3679/-
Rv3261/fbiA	(cc=0.5055)	info on Rv3261/fbiA

Correlation of Rv2431c/PE25 with Rv0456B/mazE1

Normalized LFCs for Rv2431c/PE25:
(description and provenance of datasets)

	Rv2431c/PE25	Rv0456B/mazE1
Fe_supp_jason_reseq	0.619	0.534
low_pH_jason_reseq	0.522	-0.154
NO_jason_reseq	-0.914	0.126
B6_jason_reseq	-0.36	0.382
MHCII_jason_reseq	-0.217	0.572
Isoniazid02	-0.931	-2.183
Rifampicin4	-1.6	0.471
Ethambutol3	-1.563	-1.78
Meropenem3	-1.653	-1.887
Vancomycin16	-0.921	-0.796
Rv2680_day32	-0.087	0.44
H37Rv_KO_MarP	-0.447	-0.282
hypoxia_3wks	0.582	0.0
hypoxia_6wks	0.0	-0.186
glycerol	3.461	1.014
cholesterol	6.0	0.351
AJ	1.303	-0.773
Bibs02	1.457	0.91
Bibs02c	1.199	0.929
BL6	1.457	0.719
BL6a	2.072	1.343
BXD01	0.827	0.413
BXD010	0.551	0.671
BXD011	2.085	0.891
BXD03	1.534	-0.017
BXD04	1.689	0.208
BXD05	2.296	1.222
BXD06	1.937	0.799
BXD07	2.139	0.53
BXD08	1.605	0.189
BXD09	2.05	0.657
CAST	-0.192	1.068
CCcont	1.232	0.52
DS01	3.744	0.664
DS02	3.294	0.912
DS04	3.536	0.899
DS0c	2.665	1.276
GP01	0.531	0.382
GP02	0.806	0.811
GP0c	1.557	0.062
NOD	1.523	0.962
NZO	0.962	0.152
PWK	2.947	-0.213
H37Rv_KO_CtpC	1.81	0.298
H37Rv_KO_CtpD	1.079	0.479
H37Rv_KO_Rv1272	2.011	0.329
H37Rv_KO_SugABC	1.484	0.156
H37Rv_KO_MbtN	0.09	0.13
Trans05	2.411	0.621
macrophage_unactivated	0.211	0.59
IL1	0.561	0.688
Rapamycin	0.233	1.154
Tcell	0.72	0.218
GMCSF	-0.304	-0.378
IFNab	0.668	0.438
IFNg	0.786	0.096
IFNg_GMCSF1	0.852	1.477
Rv1432_day32	0.439	0.391
Rv1565c_day32	5.482	1.046
secA2_input	-1.575	-0.139
delta_Rv3594	0.425	-0.473
delta_Rv3717	0.174	-0.406
delta_Rv3811	0.013	-0.352
delta_Rv0954	1.122	-0.279
PonA1	0.196	0.211
EccD1_KO	-0.72	-0.816
EspI_KO	-0.148	-0.57
PE35_KO	0.639	-0.193
PPE68_KO	0.64	-0.576
glycerol2	-0.013	0.154
lignocerate	-0.468	0.1
oleate	0.801	-0.16
phosphatidylcholine	0.162	0.123
acetate	-0.753	-0.332
glucAc	-0.664	0.019
Rv0950ko	0.084	0.419
Rv1096ko	-1.197	-0.332
Rv3684ko	-0.177	0.495
delta_otsA_trehalose	0.513	-0.366