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 Rv0892/-

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

	Rv1257c/-	Rv0892/-
Fe_supp_jason_reseq	1.328	2.0
low_pH_jason_reseq	0.099	0.146
NO_jason_reseq	1.168	0.0
B6_jason_reseq	0.427	1.447
MHCII_jason_reseq	0.234	0.126
Isoniazid02	1.196	-0.333
Rifampicin4	0.179	0.114
Ethambutol3	1.164	0.0
Meropenem3	-0.125	1.435
Vancomycin16	0.088	0.218
Rv2680_day32	-0.586	-0.406
H37Rv_KO_MarP	0.694	0.0
hypoxia_3wks	0.096	0.207
hypoxia_6wks	0.05	-0.228
glycerol	-0.339	-0.831
cholesterol	-0.371	0.035
AJ	0.047	0.0
Bibs02	-0.518	0.699
Bibs02c	0.85	1.096
BL6	-0.725	0.796
BL6a	1.102	1.336
BXD01	0.6	0.408
BXD010	1.13	1.116
BXD011	0.207	0.53
BXD03	0.471	0.805
BXD04	-0.052	0.554
BXD05	0.041	0.745
BXD06	0.157	0.884
BXD07	0.309	0.881
BXD08	0.193	0.317
BXD09	-0.153	0.856
CAST	0.205	0.592
CCcont	-0.215	0.0
DS01	0.527	1.237
DS02	0.485	0.904
DS04	-0.326	0.807
DS0c	0.773	0.792
GP01	-0.393	-0.559
GP02	0.338	-0.507
GP0c	0.634	-0.065
NOD	1.604	0.62
NZO	0.377	-1.215
PWK	0.266	0.226
H37Rv_KO_CtpC	0.672	0.99
H37Rv_KO_CtpD	0.051	1.402
H37Rv_KO_Rv1272	-0.272	0.539
H37Rv_KO_SugABC	0.088	1.063
H37Rv_KO_MbtN	-1.173	0.14
Trans05	0.28	0.741
macrophage_unactivated	-0.073	0.193
IL1	0.483	0.881
Rapamycin	-0.037	0.126
Tcell	0.147	-0.068
GMCSF	-0.092	-0.055
IFNab	0.647	-0.063
IFNg	-0.708	0.0
IFNg_GMCSF1	-0.792	0.314
Rv1432_day32	-0.321	-0.553
Rv1565c_day32	-0.027	-0.227
secA2_input	-1.268	-0.639
delta_Rv3594	-0.564	-0.05
delta_Rv3717	-0.561	-0.174
delta_Rv3811	-0.76	-0.1
delta_Rv0954	0.0	0.238
PonA1	-0.155	0.037
EccD1_KO	-0.043	0.704
EspI_KO	0.451	0.539
PE35_KO	0.219	0.837
PPE68_KO	-0.042	0.442
glycerol2	-1.149	-0.923
lignocerate	-0.606	-0.947
oleate	-0.922	-0.034
phosphatidylcholine	-0.437	-0.536
acetate	-0.6	-0.485
glucAc	-0.632	-1.084
Rv0950ko	0.371	0.887
Rv1096ko	0.914	0.271
Rv3684ko	0.684	0.075
delta_otsA_trehalose	0.429	-1.314