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 Rv3353c/-:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv0008c/-	(cc=0.727)	info on Rv0008c/-
Rv0278c/PE_PGRS3	(cc=0.7017)	info on Rv0278c/PE_PGRS3
Rv2426c/-	(cc=0.6969)	info on Rv2426c/-
Rv2657c/-	(cc=0.6947)	info on Rv2657c/-
Rv1160/mutT2	(cc=0.6899)	info on Rv1160/mutT2
Rv3705A/-	(cc=0.6744)	info on Rv3705A/-
Rv0887c/-	(cc=0.6722)	info on Rv0887c/-
Rv2638/-	(cc=0.6628)	info on Rv2638/-
Rv3395c/-	(cc=0.6564)	info on Rv3395c/-
Rv2499c/-	(cc=0.6468)	info on Rv2499c/-

Correlation of Rv3353c/- with Rv0008c/-

Normalized LFCs for Rv3353c/-:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3353c/-	Rv0008c/-
Fe_supp_jason_reseq	-0.717	-2.052
low_pH_jason_reseq	-0.11	-0.85
NO_jason_reseq	-0.278	1.575
B6_jason_reseq	0.221	2.298
MHCII_jason_reseq	1.201	1.965
Isoniazid02	-0.202	0.56
Rifampicin4	-0.376	0.412
Ethambutol3	-0.405	0.27
Meropenem3	-0.026	-0.231
Vancomycin16	0.172	0.979
Rv2680_day32	-1.07	0.0
H37Rv_KO_MarP	0.638	0.113
hypoxia_3wks	-0.478	-0.702
hypoxia_6wks	-1.063	-0.1
glycerol	0.846	0.856
cholesterol	0.675	0.366
AJ	0.62	0.449
Bibs02	0.603	1.347
Bibs02c	-0.582	-0.973
BL6	-0.568	-0.648
BL6a	-0.494	-3.221
BXD01	-1.238	-1.653
BXD010	-2.853	-2.357
BXD011	-0.857	-2.539
BXD03	-0.144	-1.169
BXD04	-1.562	-3.059
BXD05	-1.466	-0.609
BXD06	-1.137	-1.85
BXD07	-1.715	-1.757
BXD08	-1.122	-1.279
BXD09	-1.577	-1.863
CAST	0.127	0.349
CCcont	-0.098	-0.603
DS01	-0.137	0.186
DS02	-0.471	-0.263
DS04	0.793	1.214
DS0c	-0.572	-0.955
GP01	-0.708	0.797
GP02	0.932	-0.164
GP0c	-2.083	1.374
NOD	0.848	0.762
NZO	0.533	-0.241
PWK	0.443	0.965
H37Rv_KO_CtpC	0.684	-0.258
H37Rv_KO_CtpD	0.211	1.101
H37Rv_KO_Rv1272	-0.093	0.282
H37Rv_KO_SugABC	-2.271	0.062
H37Rv_KO_MbtN	-1.938	-1.337
Trans05	-0.616	-1.893
macrophage_unactivated	-1.218	-0.83
IL1	-3.1	-1.978
Rapamycin	-1.553	-0.43
Tcell	-1.548	-2.923
GMCSF	-1.45	-1.993
IFNab	-3.205	-2.283
IFNg	-4.196	-3.127
IFNg_GMCSF1	-0.591	-1.034
Rv1432_day32	0.0	0.755
Rv1565c_day32	-0.504	0.0
secA2_input	-0.712	-2.232
delta_Rv3594	-0.595	0.601
delta_Rv3717	0.132	1.058
delta_Rv3811	0.8	-1.393
delta_Rv0954	1.271	-0.368
PonA1	1.024	0.12
EccD1_KO	0.358	-0.362
EspI_KO	-0.471	-0.893
PE35_KO	-0.866	-0.248
PPE68_KO	-0.682	0.362
glycerol2	2.969	2.742
lignocerate	3.989	3.004
oleate	-1.691	0.788
phosphatidylcholine	2.968	2.22
acetate	3.361	4.201
glucAc	2.601	2.715
Rv0950ko	-0.826	1.158
Rv1096ko	0.905	1.583
Rv3684ko	2.112	2.103
delta_otsA_trehalose	-0.27	0.711