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 Rv3507/PE_PGRS53:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv1004c/-	(cc=0.5422)	info on Rv1004c/-
Rv1452c/PE_PGRS28	(cc=0.5389)	info on Rv1452c/PE_PGRS28
Rv0317c/glpQ2	(cc=0.5358)	info on Rv0317c/glpQ2
Rv0578c/PE_PGRS7	(cc=0.4913)	info on Rv0578c/PE_PGRS7
Rv3345c/PE_PGRS50	(cc=0.4823)	info on Rv3345c/PE_PGRS50
Rv3401/-	(cc=0.4776)	info on Rv3401/-
Rv0279c/PE_PGRS4	(cc=0.4775)	info on Rv0279c/PE_PGRS4
Rv1781c/malQ	(cc=0.4722)	info on Rv1781c/malQ
Rv1818c/PE_PGRS33	(cc=0.4678)	info on Rv1818c/PE_PGRS33
Rv2066/cobI	(cc=0.4653)	info on Rv2066/cobI

Correlation of Rv3507/PE_PGRS53 with Rv1004c/-

Normalized LFCs for Rv3507/PE_PGRS53:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3507/PE_PGRS53	Rv1004c/-
Fe_supp_jason_reseq	-0.614	-0.445
low_pH_jason_reseq	0.043	-0.674
NO_jason_reseq	-0.139	0.039
B6_jason_reseq	-0.47	-0.394
MHCII_jason_reseq	0.075	0.324
Isoniazid02	-0.083	-0.093
Rifampicin4	0.812	0.165
Ethambutol3	0.665	1.51
Meropenem3	0.829	0.527
Vancomycin16	0.35	0.379
Rv2680_day32	0.814	0.138
H37Rv_KO_MarP	0.47	0.33
hypoxia_3wks	0.207	0.279
hypoxia_6wks	-0.687	-0.39
glycerol	1.441	0.714
cholesterol	1.125	0.292
AJ	0.57	0.81
Bibs02	0.449	0.138
Bibs02c	0.584	0.493
BL6	-0.642	-1.506
BL6a	-0.131	-0.036
BXD01	-0.057	-0.184
BXD010	-0.114	-0.421
BXD011	-0.653	-0.985
BXD03	0.057	-0.423
BXD04	-0.511	0.212
BXD05	-0.058	-0.41
BXD06	-0.355	-0.718
BXD07	-0.446	-0.274
BXD08	-0.317	0.151
BXD09	-0.335	-1.141
CAST	0.527	-0.232
CCcont	-0.317	-1.537
DS01	-0.563	0.429
DS02	0.0	0.35
DS04	0.342	1.043
DS0c	0.135	-0.162
GP01	1.147	0.82
GP02	0.955	0.257
GP0c	0.405	0.349
NOD	1.209	0.013
NZO	0.0	-0.863
PWK	-0.129	-0.402
H37Rv_KO_CtpC	0.506	0.048
H37Rv_KO_CtpD	0.944	0.852
H37Rv_KO_Rv1272	0.461	0.042
H37Rv_KO_SugABC	-0.348	-0.087
H37Rv_KO_MbtN	0.487	-0.348
Trans05	0.635	0.422
macrophage_unactivated	0.524	-1.032
IL1	0.0	-0.584
Rapamycin	-0.11	-1.132
Tcell	-0.613	-0.935
GMCSF	0.182	-1.048
IFNab	-0.816	-1.56
IFNg	0.184	-1.636
IFNg_GMCSF1	0.421	-1.477
Rv1432_day32	0.266	0.799
Rv1565c_day32	-0.069	-0.725
secA2_input	-0.285	-0.584
delta_Rv3594	-0.13	-0.119
delta_Rv3717	0.574	0.165
delta_Rv3811	0.678	0.235
delta_Rv0954	-0.11	0.019
PonA1	0.323	-0.166
EccD1_KO	-0.375	-0.125
EspI_KO	-0.411	-0.054
PE35_KO	-1.041	-1.205
PPE68_KO	-1.312	-1.376
glycerol2	-0.261	-0.448
lignocerate	-0.197	-0.492
oleate	-0.23	0.539
phosphatidylcholine	-0.406	0.09
acetate	-0.667	-0.637
glucAc	0.044	-0.92
Rv0950ko	0.359	-0.121
Rv1096ko	0.525	-0.072
Rv3684ko	0.39	-0.897
delta_otsA_trehalose	0.27	-0.838