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 Rv1257c/-:

update plot	correlation	link to info on gene
Rv2334/cysK1	(cc=0.4709)	info on Rv2334/cysK1
Rv2335/cysE	(cc=0.4236)	info on Rv2335/cysE
Rv0321/dcd	(cc=0.4208)	info on Rv0321/dcd
Rv1778c/-	(cc=0.4194)	info on Rv1778c/-
Rv1681/moeX	(cc=0.4127)	info on Rv1681/moeX
Rv3466/-	(cc=0.4097)	info on Rv3466/-
Rv0892/-	(cc=0.405)	info on Rv0892/-
Rv0526/-	(cc=0.3951)	info on Rv0526/-
Rv3714c/-	(cc=0.3919)	info on Rv3714c/-
Rv0078/-	(cc=0.3893)	info on Rv0078/-

Correlation of Rv1257c/- with Rv2334/cysK1

Normalized LFCs for Rv1257c/-:
(description and provenance of datasets)

	Rv1257c/-	Rv2334/cysK1
Fe_supp_jason_reseq	1.328	2.437
low_pH_jason_reseq	0.099	5.069
NO_jason_reseq	1.168	1.089
B6_jason_reseq	0.427	0.357
MHCII_jason_reseq	0.234	-0.257
Isoniazid02	1.196	3.403
Rifampicin4	0.179	0.634
Ethambutol3	1.164	0.285
Meropenem3	-0.125	-0.335
Vancomycin16	0.088	0.809
Rv2680_day32	-0.586	0.0
H37Rv_KO_MarP	0.694	1.666
hypoxia_3wks	0.096	-1.284
hypoxia_6wks	0.05	0.378
glycerol	-0.339	2.455
cholesterol	-0.371	1.761
AJ	0.047	0.232
Bibs02	-0.518	0.0
Bibs02c	0.85	0.0
BL6	-0.725	0.53
BL6a	1.102	1.435
BXD01	0.6	2.245
BXD010	1.13	1.115
BXD011	0.207	0.626
BXD03	0.471	1.351
BXD04	-0.052	1.184
BXD05	0.041	1.109
BXD06	0.157	1.485
BXD07	0.309	0.768
BXD08	0.193	2.419
BXD09	-0.153	0.863
CAST	0.205	3.337
CCcont	-0.215	1.492
DS01	0.527	0.45
DS02	0.485	0.217
DS04	-0.326	0.37
DS0c	0.773	0.0
GP01	-0.393	0.0
GP02	0.338	0.0
GP0c	0.634	0.0
NOD	1.604	1.507
NZO	0.377	0.0
PWK	0.266	0.196
H37Rv_KO_CtpC	0.672	0.0
H37Rv_KO_CtpD	0.051	0.703
H37Rv_KO_Rv1272	-0.272	0.269
H37Rv_KO_SugABC	0.088	0.664
H37Rv_KO_MbtN	-1.173	0.283
Trans05	0.28	0.803
macrophage_unactivated	-0.073	0.398
IL1	0.483	-0.409
Rapamycin	-0.037	-0.424
Tcell	0.147	-0.45
GMCSF	-0.092	0.0
IFNab	0.647	-0.417
IFNg	-0.708	-0.369
IFNg_GMCSF1	-0.792	0.0
Rv1432_day32	-0.321	-0.18
Rv1565c_day32	-0.027	1.507
secA2_input	-1.268	-1.315
delta_Rv3594	-0.564	-2.522
delta_Rv3717	-0.561	-2.896
delta_Rv3811	-0.76	-2.767
delta_Rv0954	0.0	-0.716
PonA1	-0.155	0.864
EccD1_KO	-0.043	0.526
EspI_KO	0.451	2.053
PE35_KO	0.219	0.683
PPE68_KO	-0.042	1.59
glycerol2	-1.149	-1.208
lignocerate	-0.606	-0.756
oleate	-0.922	-1.418
phosphatidylcholine	-0.437	-1.401
acetate	-0.6	0.72
glucAc	-0.632	0.272
Rv0950ko	0.371	1.999
Rv1096ko	0.914	2.925
Rv3684ko	0.684	2.044
delta_otsA_trehalose	0.429	0.854