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 Rv3653/PE_PGRS61:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv1087/PE_PGRS21	(cc=0.6856)	info on Rv1087/PE_PGRS21
Rv3897c/-	(cc=0.615)	info on Rv3897c/-
Rv1818c/PE_PGRS33	(cc=0.6066)	info on Rv1818c/PE_PGRS33
Rv1091/PE_PGRS22	(cc=0.5882)	info on Rv1091/PE_PGRS22
Rv2841c/nusA	(cc=0.5841)	info on Rv2841c/nusA
Rv2490c/PE_PGRS43	(cc=0.5807)	info on Rv2490c/PE_PGRS43
Rv0649/fabD2	(cc=0.5774)	info on Rv0649/fabD2
Rv0297/PE_PGRS5	(cc=0.5617)	info on Rv0297/PE_PGRS5
Rv1763/-	(cc=0.556)	info on Rv1763/-
Rv0850/-	(cc=0.5545)	info on Rv0850/-

Correlation of Rv3653/PE_PGRS61 with Rv1087/PE_PGRS21

Normalized LFCs for Rv3653/PE_PGRS61:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3653/PE_PGRS61	Rv1087/PE_PGRS21
Fe_supp_jason_reseq	-1.751	-1.443
low_pH_jason_reseq	0.796	-1.295
NO_jason_reseq	-1.376	-0.431
B6_jason_reseq	-0.998	-0.404
MHCII_jason_reseq	0.838	-0.066
Isoniazid02	-0.097	-1.653
Rifampicin4	0.653	0.214
Ethambutol3	-0.505	0.196
Meropenem3	-0.208	-0.639
Vancomycin16	0.0	-0.865
Rv2680_day32	0.131	0.842
H37Rv_KO_MarP	-0.054	0.162
hypoxia_3wks	-0.243	-0.427
hypoxia_6wks	-1.038	-0.727
glycerol	1.796	1.262
cholesterol	0.657	0.519
AJ	2.123	1.155
Bibs02	0.207	0.782
Bibs02c	0.949	0.838
BL6	-1.513	0.186
BL6a	-0.251	0.133
BXD01	1.001	0.1
BXD010	-1.676	0.2
BXD011	-0.559	-0.79
BXD03	-0.041	0.235
BXD04	-1.184	-0.487
BXD05	-1.101	-0.492
BXD06	-1.493	0.014
BXD07	-0.809	-0.43
BXD08	-1.274	-0.431
BXD09	-0.75	-0.437
CAST	-0.537	-0.215
CCcont	-1.67	-0.173
DS01	1.205	-0.072
DS02	1.407	0.414
DS04	1.376	0.777
DS0c	-0.066	-0.11
GP01	1.378	1.227
GP02	-0.134	1.357
GP0c	1.48	0.136
NOD	0.428	0.944
NZO	-0.54	-0.144
PWK	1.0	0.358
H37Rv_KO_CtpC	-1.226	-0.461
H37Rv_KO_CtpD	0.691	1.767
H37Rv_KO_Rv1272	-0.619	0.546
H37Rv_KO_SugABC	-1.108	0.362
H37Rv_KO_MbtN	-1.067	0.196
Trans05	2.522	0.323
macrophage_unactivated	-3.857	-0.919
IL1	-4.239	-2.441
Rapamycin	-2.056	-2.734
Tcell	-3.679	-1.825
GMCSF	-4.077	-0.935
IFNab	-2.899	-2.839
IFNg	-0.345	-1.497
IFNg_GMCSF1	-2.316	-2.061
Rv1432_day32	0.85	0.568
Rv1565c_day32	-1.15	-1.084
secA2_input	-0.568	-0.551
delta_Rv3594	0.696	0.095
delta_Rv3717	1.131	-0.109
delta_Rv3811	-0.098	-0.254
delta_Rv0954	-2.367	-1.503
PonA1	-0.219	-0.04
EccD1_KO	-0.585	-0.023
EspI_KO	-0.933	-0.06
PE35_KO	0.878	0.219
PPE68_KO	-0.723	-0.138
glycerol2	1.261	0.933
lignocerate	0.673	1.382
oleate	1.55	0.366
phosphatidylcholine	0.95	0.933
acetate	1.32	1.235
glucAc	0.096	1.491
Rv0950ko	1.939	0.289
Rv1096ko	1.475	0.878
Rv3684ko	-0.344	0.57
delta_otsA_trehalose	0.0	1.004