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 Rv3223c/sigH:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv1196/PPE18	(cc=0.5787)	info on Rv1196/PPE18
Rv3232c/ppk2	(cc=0.5662)	info on Rv3232c/ppk2
Rv3433c/-	(cc=0.5645)	info on Rv3433c/-
Rv3269/-	(cc=0.5628)	info on Rv3269/-
Rv3814c/-	(cc=0.5351)	info on Rv3814c/-
Rv2352c/PPE38	(cc=0.5318)	info on Rv2352c/PPE38
Rv3133c/devR	(cc=0.5183)	info on Rv3133c/devR
Rv3161c/-	(cc=0.5146)	info on Rv3161c/-
Rv2853/PE_PGRS48	(cc=0.5123)	info on Rv2853/PE_PGRS48
Rv1504c/-	(cc=0.5112)	info on Rv1504c/-

Correlation of Rv3223c/sigH with Rv1196/PPE18

Normalized LFCs for Rv3223c/sigH:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3223c/sigH	Rv1196/PPE18
Fe_supp_jason_reseq	1.377	-0.06
low_pH_jason_reseq	-1.166	-1.091
NO_jason_reseq	-1.011	-0.914
B6_jason_reseq	-1.144	-1.217
MHCII_jason_reseq	-0.3	0.228
Isoniazid02	-0.799	2.462
Rifampicin4	-0.333	0.842
Ethambutol3	1.049	1.445
Meropenem3	-0.879	-0.121
Vancomycin16	-0.432	0.531
Rv2680_day32	-1.414	-1.276
H37Rv_KO_MarP	-0.024	-0.934
hypoxia_3wks	-1.782	0.626
hypoxia_6wks	-2.817	0.875
glycerol	1.612	0.828
cholesterol	2.7	0.379
AJ	0.432	1.657
Bibs02	1.605	0.685
Bibs02c	1.106	1.155
BL6	0.969	1.282
BL6a	1.435	1.591
BXD01	0.96	0.97
BXD010	0.554	0.644
BXD011	0.712	1.367
BXD03	1.014	1.557
BXD04	0.426	0.999
BXD05	1.074	1.494
BXD06	0.554	0.919
BXD07	0.316	0.923
BXD08	0.857	1.004
BXD09	0.677	1.004
CAST	0.707	0.863
CCcont	2.402	1.275
DS01	1.021	1.246
DS02	0.055	0.892
DS04	0.52	1.684
DS0c	2.11	1.171
GP01	1.964	0.765
GP02	0.301	0.418
GP0c	0.297	0.506
NOD	0.418	0.133
NZO	1.202	0.761
PWK	-0.509	0.999
H37Rv_KO_CtpC	1.047	-0.175
H37Rv_KO_CtpD	1.055	1.298
H37Rv_KO_Rv1272	2.343	1.113
H37Rv_KO_SugABC	1.068	1.499
H37Rv_KO_MbtN	2.627	1.065
Trans05	2.3	0.993
macrophage_unactivated	0.237	0.246
IL1	-3.45	-1.16
Rapamycin	-1.715	-0.35
Tcell	-1.352	-1.0
GMCSF	-0.51	-0.742
IFNab	0.65	1.62
IFNg	-2.405	-1.868
IFNg_GMCSF1	-1.197	-0.308
Rv1432_day32	-0.645	-0.271
Rv1565c_day32	0.317	-0.101
secA2_input	-1.633	-0.312
delta_Rv3594	1.975	0.569
delta_Rv3717	0.896	0.865
delta_Rv3811	1.619	0.758
delta_Rv0954	0.833	0.339
PonA1	-0.444	-0.369
EccD1_KO	0.444	0.122
EspI_KO	0.197	1.32
PE35_KO	0.925	0.72
PPE68_KO	1.075	0.157
glycerol2	0.68	1.103
lignocerate	0.983	0.742
oleate	0.822	-0.425
phosphatidylcholine	1.21	1.064
acetate	0.457	-0.045
glucAc	0.374	0.176
Rv0950ko	-0.06	-0.057
Rv1096ko	-0.516	-0.03
Rv3684ko	-0.711	-0.226
delta_otsA_trehalose	2.183	1.263