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 Rv3142c/-:

update plot	correlation	link to info on gene
Rv2106/-	(cc=0.7082)	info on Rv2106/-
Rv2479c/-	(cc=0.7074)	info on Rv2479c/-
Rv2279/-	(cc=0.7018)	info on Rv2279/-
Rv2355/-	(cc=0.7014)	info on Rv2355/-
Rv1764/-	(cc=0.689)	info on Rv1764/-
Rv3185/-	(cc=0.6857)	info on Rv3185/-
Rv2814c/-	(cc=0.6843)	info on Rv2814c/-
Rv3187/-	(cc=0.6772)	info on Rv3187/-
Rv2167c/-	(cc=0.6751)	info on Rv2167c/-
Rv0823c/-	(cc=0.6728)	info on Rv0823c/-

Correlation of Rv3142c/- with Rv3187/-

Normalized LFCs for Rv3142c/-:
(description and provenance of datasets)

	Rv3142c/-	Rv3187/-
Fe_supp_jason_reseq	-0.278	-0.646
low_pH_jason_reseq	-0.852	-0.571
NO_jason_reseq	0.399	0.165
B6_jason_reseq	-0.254	-0.598
MHCII_jason_reseq	-0.69	-0.095
Isoniazid02	-0.172	-0.122
Rifampicin4	0.317	0.59
Ethambutol3	0.116	0.37
Meropenem3	0.019	-0.48
Vancomycin16	0.26	-0.318
Rv2680_day32	-0.971	0.127
H37Rv_KO_MarP	-0.155	-0.147
hypoxia_3wks	0.024	0.494
hypoxia_6wks	-0.432	0.031
glycerol	-0.825	-0.772
cholesterol	0.155	0.125
AJ	1.219	1.301
Bibs02	0.257	1.102
Bibs02c	1.422	1.544
BL6	0.821	0.171
BL6a	1.653	0.954
BXD01	0.919	0.523
BXD010	1.183	0.722
BXD011	1.105	0.739
BXD03	0.324	0.722
BXD04	0.606	0.458
BXD05	1.049	0.933
BXD06	0.946	0.424
BXD07	1.398	0.835
BXD08	0.626	0.411
BXD09	0.913	0.642
CAST	1.303	1.078
CCcont	0.784	-0.034
DS01	0.79	0.739
DS02	0.521	0.788
DS04	0.512	1.003
DS0c	0.793	0.919
GP01	0.674	1.172
GP02	0.388	1.381
GP0c	0.362	0.613
NOD	1.084	1.222
NZO	0.64	1.017
PWK	1.186	1.206
H37Rv_KO_CtpC	1.517	0.725
H37Rv_KO_CtpD	1.639	0.739
H37Rv_KO_Rv1272	1.18	0.516
H37Rv_KO_SugABC	1.178	0.718
H37Rv_KO_MbtN	1.207	0.54
Trans05	1.301	0.823
macrophage_unactivated	0.104	-0.609
IL1	-0.872	-0.38
Rapamycin	-0.353	-0.371
Tcell	-0.186	-0.951
GMCSF	-0.655	-0.069
IFNab	-0.871	-0.883
IFNg	0.326	-0.211
IFNg_GMCSF1	-0.088	-0.104
Rv1432_day32	-0.061	0.443
Rv1565c_day32	0.204	0.073
secA2_input	0.059	0.202
delta_Rv3594	-0.268	-0.118
delta_Rv3717	-0.294	-0.234
delta_Rv3811	0.092	-0.012
delta_Rv0954	-0.322	0.368
PonA1	0.167	0.047
EccD1_KO	-0.342	-0.023
EspI_KO	0.211	0.856
PE35_KO	0.3	0.712
PPE68_KO	0.218	0.579
glycerol2	-0.092	-0.961
lignocerate	0.754	-0.745
oleate	-0.411	-1.15
phosphatidylcholine	-0.022	-0.916
acetate	0.213	-0.163
glucAc	0.495	0.088
Rv0950ko	1.462	0.229
Rv1096ko	0.072	0.712
Rv3684ko	0.229	-0.364
delta_otsA_trehalose	0.14	-0.052