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 Rv0049/-:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv3854c/ethA	(cc=0.6401)	info on Rv3854c/ethA
Rv1640c/lysX	(cc=0.5913)	info on Rv1640c/lysX
Rv0924c/mntH	(cc=0.5791)	info on Rv0924c/mntH
Rv1836c/-	(cc=0.5782)	info on Rv1836c/-
Rv1925/fadD31	(cc=0.5751)	info on Rv1925/fadD31
Rv2462c/tig	(cc=0.573)	info on Rv2462c/tig
Rv3919c/gid	(cc=0.5704)	info on Rv3919c/gid
Rv1111c/-	(cc=0.554)	info on Rv1111c/-
Rv2993c/-	(cc=0.5512)	info on Rv2993c/-
Rv2190c/-	(cc=0.5407)	info on Rv2190c/-

Correlation of Rv0049/- with Rv3854c/ethA

Normalized LFCs for Rv0049/-:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv0049/-	Rv3854c/ethA
Fe_supp_jason_reseq	0.404	0.998
low_pH_jason_reseq	-0.361	-0.467
NO_jason_reseq	2.237	0.683
B6_jason_reseq	2.761	-0.283
MHCII_jason_reseq	1.686	0.123
Isoniazid02	-4.265	-0.387
Rifampicin4	-2.889	-0.382
Ethambutol3	-4.182	-0.039
Meropenem3	-1.01	-0.346
Vancomycin16	-6.0	-0.767
Rv2680_day32	-1.252	0.22
H37Rv_KO_MarP	-5.444	-1.053
hypoxia_3wks	-0.546	-0.032
hypoxia_6wks	-1.334	-0.033
glycerol	0.774	-0.385
cholesterol	1.774	0.709
AJ	0.889	-0.788
Bibs02	-2.229	0.201
Bibs02c	-0.308	-0.092
BL6	1.028	0.606
BL6a	2.627	0.933
BXD01	2.217	0.281
BXD010	2.728	0.77
BXD011	4.652	0.723
BXD03	3.087	1.176
BXD04	2.028	0.639
BXD05	3.906	1.269
BXD06	4.436	1.119
BXD07	4.021	0.804
BXD08	2.172	0.326
BXD09	2.471	0.918
CAST	-1.203	-0.247
CCcont	2.649	0.588
DS01	-1.921	0.275
DS02	-2.774	0.391
DS04	0.575	0.188
DS0c	-2.211	0.016
GP01	1.773	0.561
GP02	2.935	0.572
GP0c	3.495	0.787
NOD	-1.515	-0.428
NZO	1.376	0.272
PWK	3.436	0.203
H37Rv_KO_CtpC	1.75	0.506
H37Rv_KO_CtpD	-1.411	1.09
H37Rv_KO_Rv1272	2.554	1.067
H37Rv_KO_SugABC	2.361	1.875
H37Rv_KO_MbtN	4.289	0.978
Trans05	1.424	0.77
macrophage_unactivated	0.268	0.492
IL1	1.092	0.169
Rapamycin	-0.42	0.107
Tcell	2.9	0.277
GMCSF	-2.044	0.298
IFNab	-1.811	0.257
IFNg	0.043	0.673
IFNg_GMCSF1	-0.949	0.355
Rv1432_day32	4.133	0.454
Rv1565c_day32	0.218	-0.025
secA2_input	2.224	0.288
delta_Rv3594	6.0	0.649
delta_Rv3717	6.0	1.076
delta_Rv3811	5.737	1.147
delta_Rv0954	4.229	0.171
PonA1	1.526	0.143
EccD1_KO	-0.763	0.253
EspI_KO	-0.257	-0.317
PE35_KO	-1.062	-0.615
PPE68_KO	0.47	-0.109
glycerol2	0.227	-0.493
lignocerate	-1.453	-0.235
oleate	-1.11	-0.179
phosphatidylcholine	-1.426	-0.43
acetate	0.347	-0.321
glucAc	0.216	-0.429
Rv0950ko	-0.461	0.639
Rv1096ko	0.308	0.274
Rv3684ko	1.618	0.874
delta_otsA_trehalose	-0.75	-0.014