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 Rv1729c/-:

update plot	correlation	link to info on gene
Rv3398c/idsA1	(cc=0.6624)	info on Rv3398c/idsA1
Rv0844c/narL	(cc=0.6417)	info on Rv0844c/narL
Rv1664/pks9	(cc=0.6371)	info on Rv1664/pks9
Rv3759c/proX	(cc=0.5882)	info on Rv3759c/proX
Rv1021/-	(cc=0.5861)	info on Rv1021/-
Rv1551/plsB1	(cc=0.5828)	info on Rv1551/plsB1
Rv1616/-	(cc=0.5771)	info on Rv1616/-
Rv1891/-	(cc=0.5598)	info on Rv1891/-
Rv3146/nuoB	(cc=0.5528)	info on Rv3146/nuoB
Rv1870c/-	(cc=0.55)	info on Rv1870c/-

Correlation of Rv1729c/- with Rv0844c/narL

Normalized LFCs for Rv1729c/-:
(description and provenance of datasets)

	Rv1729c/-	Rv0844c/narL
Fe_supp_jason_reseq	0.158	-0.821
low_pH_jason_reseq	0.673	-0.885
NO_jason_reseq	0.197	-0.798
B6_jason_reseq	-0.947	-1.434
MHCII_jason_reseq	-1.6	-1.717
Isoniazid02	0.41	-0.1
Rifampicin4	0.103	0.208
Ethambutol3	2.122	1.001
Meropenem3	0.45	0.189
Vancomycin16	0.748	-0.342
Rv2680_day32	0.659	0.584
H37Rv_KO_MarP	0.667	0.126
hypoxia_3wks	0.427	-0.167
hypoxia_6wks	-0.159	-0.334
glycerol	0.686	1.508
cholesterol	-0.398	0.542
AJ	-0.297	0.509
Bibs02	-1.183	-0.719
Bibs02c	-0.467	-0.943
BL6	1.501	1.836
BL6a	0.673	1.204
BXD01	0.48	0.829
BXD010	1.79	0.842
BXD011	1.392	1.187
BXD03	1.691	1.108
BXD04	1.224	1.469
BXD05	1.199	0.771
BXD06	1.382	0.426
BXD07	1.552	0.737
BXD08	1.23	1.32
BXD09	1.475	1.096
CAST	-0.095	0.282
CCcont	1.406	1.334
DS01	-0.197	0.224
DS02	0.4	-0.191
DS04	0.873	-0.17
DS0c	0.248	-0.358
GP01	1.093	1.085
GP02	0.064	2.145
GP0c	1.136	1.153
NOD	-0.864	-0.884
NZO	-0.445	0.337
PWK	-0.438	-0.254
H37Rv_KO_CtpC	1.041	1.893
H37Rv_KO_CtpD	0.502	1.565
H37Rv_KO_Rv1272	2.178	2.107
H37Rv_KO_SugABC	1.968	1.083
H37Rv_KO_MbtN	0.827	1.304
Trans05	2.694	1.91
macrophage_unactivated	1.108	0.707
IL1	2.186	0.507
Rapamycin	0.976	0.319
Tcell	0.635	0.417
GMCSF	1.217	1.127
IFNab	1.439	0.753
IFNg	0.938	0.214
IFNg_GMCSF1	0.317	0.277
Rv1432_day32	0.0	0.675
Rv1565c_day32	0.951	0.215
secA2_input	-1.442	-0.549
delta_Rv3594	-0.196	-0.912
delta_Rv3717	-0.751	-0.745
delta_Rv3811	-0.19	-1.019
delta_Rv0954	-0.678	-0.574
PonA1	-0.733	-0.895
EccD1_KO	-1.223	-0.03
EspI_KO	0.183	0.876
PE35_KO	1.015	0.528
PPE68_KO	1.277	0.627
glycerol2	-0.727	0.659
lignocerate	-0.632	0.951
oleate	-0.421	1.168
phosphatidylcholine	-0.597	0.808
acetate	0.264	-0.136
glucAc	0.164	0.086
Rv0950ko	0.694	-0.075
Rv1096ko	1.475	0.169
Rv3684ko	-0.789	-0.429
delta_otsA_trehalose	-0.778	-1.055