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 Rv0342/iniA:

update plot	correlation	link to info on gene
Rv0968/-	(cc=0.6427)	info on Rv0968/-
Rv2679/echA15	(cc=0.6294)	info on Rv2679/echA15
Rv3329/-	(cc=0.6205)	info on Rv3329/-
Rv0160c/PE4	(cc=0.6199)	info on Rv0160c/PE4
Rv0940c/-	(cc=0.5886)	info on Rv0940c/-
Rv3312c/-	(cc=0.587)	info on Rv3312c/-
Rv3508/PE_PGRS54	(cc=0.5785)	info on Rv3508/PE_PGRS54
Rv0399c/lpqK	(cc=0.578)	info on Rv0399c/lpqK
Rv0115/hddA	(cc=0.5757)	info on Rv0115/hddA
Rv3406/-	(cc=0.5703)	info on Rv3406/-

Correlation of Rv0342/iniA with Rv3406/-

Normalized LFCs for Rv0342/iniA:
(description and provenance of datasets)

	Rv0342/iniA	Rv3406/-
Fe_supp_jason_reseq	-0.583	-0.343
low_pH_jason_reseq	-0.781	-0.477
NO_jason_reseq	0.795	-0.347
B6_jason_reseq	0.252	-0.298
MHCII_jason_reseq	0.5	0.298
Isoniazid02	-2.219	-1.986
Rifampicin4	0.33	0.368
Ethambutol3	-2.382	-1.893
Meropenem3	-1.242	-0.167
Vancomycin16	-0.7	-0.748
Rv2680_day32	-0.18	-0.062
H37Rv_KO_MarP	0.368	0.524
hypoxia_3wks	-0.112	-0.032
hypoxia_6wks	-0.535	-0.386
glycerol	0.532	0.023
cholesterol	0.446	-0.246
AJ	0.765	0.531
Bibs02	0.009	0.201
Bibs02c	-0.656	-0.662
BL6	-0.238	1.034
BL6a	-0.331	0.145
BXD01	-0.119	-0.008
BXD010	-0.076	0.811
BXD011	0.106	0.153
BXD03	0.207	-0.158
BXD04	0.058	0.425
BXD05	0.414	0.565
BXD06	0.387	0.274
BXD07	-0.097	0.336
BXD08	0.05	0.023
BXD09	-0.062	0.494
CAST	0.322	0.46
CCcont	-0.276	0.043
DS01	-0.477	0.31
DS02	0.221	-0.05
DS04	-0.646	0.077
DS0c	0.489	-0.239
GP01	0.527	0.288
GP02	0.28	1.221
GP0c	0.068	-0.528
NOD	0.042	0.809
NZO	0.549	-0.194
PWK	0.517	0.512
H37Rv_KO_CtpC	0.207	-0.067
H37Rv_KO_CtpD	-0.05	0.795
H37Rv_KO_Rv1272	0.588	-0.911
H37Rv_KO_SugABC	0.512	0.155
H37Rv_KO_MbtN	0.24	-0.211
Trans05	0.793	-0.565
macrophage_unactivated	-0.429	-0.331
IL1	-0.35	0.039
Rapamycin	0.147	-0.04
Tcell	-0.081	0.124
GMCSF	-0.312	0.195
IFNab	0.239	-0.218
IFNg	-0.155	0.449
IFNg_GMCSF1	0.176	0.251
Rv1432_day32	0.186	0.252
Rv1565c_day32	0.39	-0.24
secA2_input	0.564	-0.016
delta_Rv3594	-0.509	-0.465
delta_Rv3717	-0.352	-0.262
delta_Rv3811	-0.495	-0.149
delta_Rv0954	-0.351	0.419
PonA1	-0.163	0.259
EccD1_KO	0.023	0.691
EspI_KO	-0.522	0.046
PE35_KO	-0.292	-0.047
PPE68_KO	-0.659	-0.211
glycerol2	0.423	0.553
lignocerate	0.66	0.225
oleate	0.461	0.527
phosphatidylcholine	0.391	0.5
acetate	0.632	0.219
glucAc	0.381	0.06
Rv0950ko	0.286	0.573
Rv1096ko	0.531	0.694
Rv3684ko	0.311	0.151
delta_otsA_trehalose	1.165	1.329