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 Rv2106/-

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

	Rv3142c/-	Rv2106/-
Fe_supp_jason_reseq	-0.278	-0.358
low_pH_jason_reseq	-0.852	-0.087
NO_jason_reseq	0.399	-0.076
B6_jason_reseq	-0.254	-0.398
MHCII_jason_reseq	-0.69	-0.022
Isoniazid02	-0.172	0.173
Rifampicin4	0.317	1.132
Ethambutol3	0.116	0.707
Meropenem3	0.019	0.122
Vancomycin16	0.26	0.066
Rv2680_day32	-0.971	-0.014
H37Rv_KO_MarP	-0.155	-0.096
hypoxia_3wks	0.024	0.407
hypoxia_6wks	-0.432	-0.044
glycerol	-0.825	-0.513
cholesterol	0.155	0.163
AJ	1.219	1.277
Bibs02	0.257	1.178
Bibs02c	1.422	1.845
BL6	0.821	0.18
BL6a	1.653	1.131
BXD01	0.919	0.722
BXD010	1.183	0.928
BXD011	1.105	0.985
BXD03	0.324	0.804
BXD04	0.606	0.524
BXD05	1.049	1.108
BXD06	0.946	0.539
BXD07	1.398	0.852
BXD08	0.626	0.568
BXD09	0.913	0.892
CAST	1.303	1.393
CCcont	0.784	0.276
DS01	0.79	1.047
DS02	0.521	0.929
DS04	0.512	1.134
DS0c	0.793	1.298
GP01	0.674	1.037
GP02	0.388	1.26
GP0c	0.362	0.702
NOD	1.084	1.573
NZO	0.64	1.055
PWK	1.186	1.199
H37Rv_KO_CtpC	1.517	0.911
H37Rv_KO_CtpD	1.639	0.887
H37Rv_KO_Rv1272	1.18	0.547
H37Rv_KO_SugABC	1.178	0.888
H37Rv_KO_MbtN	1.207	0.738
Trans05	1.301	0.838
macrophage_unactivated	0.104	-0.559
IL1	-0.872	-0.546
Rapamycin	-0.353	-0.786
Tcell	-0.186	-0.88
GMCSF	-0.655	-0.253
IFNab	-0.871	-0.91
IFNg	0.326	-0.529
IFNg_GMCSF1	-0.088	-0.258
Rv1432_day32	-0.061	0.441
Rv1565c_day32	0.204	0.281
secA2_input	0.059	-0.193
delta_Rv3594	-0.268	0.064
delta_Rv3717	-0.294	-0.166
delta_Rv3811	0.092	0.122
delta_Rv0954	-0.322	0.655
PonA1	0.167	-0.02
EccD1_KO	-0.342	0.214
EspI_KO	0.211	0.85
PE35_KO	0.3	0.782
PPE68_KO	0.218	0.448
glycerol2	-0.092	-0.541
lignocerate	0.754	-0.459
oleate	-0.411	-0.693
phosphatidylcholine	-0.022	-0.482
acetate	0.213	-0.098
glucAc	0.495	-0.061
Rv0950ko	1.462	0.184
Rv1096ko	0.072	0.057
Rv3684ko	0.229	-0.062
delta_otsA_trehalose	0.14	0.35