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 Rv0319/pcp:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv0616A/vapB29	(cc=0.6195)	info on Rv0616A/vapB29
Rv0749/vapC31	(cc=0.5839)	info on Rv0749/vapC31
Rv1359/-	(cc=0.5552)	info on Rv1359/-
Rv2499c/-	(cc=0.5521)	info on Rv2499c/-
Rv0899/ompA	(cc=0.5454)	info on Rv0899/ompA
Rv3395c/-	(cc=0.5313)	info on Rv3395c/-
Rv2212/-	(cc=0.5298)	info on Rv2212/-
Rv3059/cyp136	(cc=0.5297)	info on Rv3059/cyp136
Rv3083/-	(cc=0.5096)	info on Rv3083/-
Rv0887c/-	(cc=0.5031)	info on Rv0887c/-

Correlation of Rv0319/pcp with Rv0616A/vapB29

Normalized LFCs for Rv0319/pcp:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv0319/pcp	Rv0616A/vapB29
Fe_supp_jason_reseq	0.29	0.635
low_pH_jason_reseq	1.109	-1.066
NO_jason_reseq	0.058	-1.089
B6_jason_reseq	0.452	0.057
MHCII_jason_reseq	0.777	1.027
Isoniazid02	0.895	-0.53
Rifampicin4	0.636	-2.708
Ethambutol3	0.209	-1.721
Meropenem3	0.0	-1.538
Vancomycin16	0.499	-1.287
Rv2680_day32	-0.121	0.473
H37Rv_KO_MarP	0.034	0.299
hypoxia_3wks	0.363	-2.165
hypoxia_6wks	0.106	-1.036
glycerol	0.0	-0.796
cholesterol	0.12	-0.783
AJ	0.289	-1.309
Bibs02	-0.748	-0.564
Bibs02c	0.344	-0.059
BL6	0.367	0.71
BL6a	0.077	-1.231
BXD01	-0.092	-3.352
BXD010	0.211	-2.113
BXD011	0.065	-1.331
BXD03	0.14	-1.267
BXD04	-0.367	-2.682
BXD05	0.924	-0.441
BXD06	-0.251	-2.329
BXD07	-0.233	-2.639
BXD08	-0.278	-1.06
BXD09	-0.284	-2.72
CAST	-0.265	1.89
CCcont	0.495	-1.299
DS01	0.491	-0.881
DS02	0.145	0.375
DS04	-0.714	-2.35
DS0c	0.501	-1.958
GP01	0.022	-2.932
GP02	-1.296	-0.706
GP0c	-0.648	-1.83
NOD	0.488	0.182
NZO	-0.767	-0.666
PWK	0.131	-0.372
H37Rv_KO_CtpC	-0.824	-1.466
H37Rv_KO_CtpD	-2.477	-3.192
H37Rv_KO_Rv1272	-1.818	-3.483
H37Rv_KO_SugABC	-0.776	-0.939
H37Rv_KO_MbtN	-0.808	-1.432
Trans05	-0.917	-0.916
macrophage_unactivated	0.161	-2.007
IL1	0.027	-1.323
Rapamycin	0.157	-1.765
Tcell	0.583	-1.32
GMCSF	-0.285	0.306
IFNab	-0.738	-0.837
IFNg	-0.214	0.134
IFNg_GMCSF1	0.16	-1.313
Rv1432_day32	0.541	-0.475
Rv1565c_day32	0.971	0.265
secA2_input	0.574	-1.853
delta_Rv3594	1.23	0.702
delta_Rv3717	1.056	0.405
delta_Rv3811	1.108	1.939
delta_Rv0954	1.795	1.799
PonA1	2.507	2.649
EccD1_KO	0.069	0.194
EspI_KO	0.63	-2.073
PE35_KO	-0.315	-2.121
PPE68_KO	0.79	-1.078
glycerol2	1.77	0.0
lignocerate	2.289	1.61
oleate	0.457	0.196
phosphatidylcholine	1.923	0.531
acetate	1.662	2.382
glucAc	1.437	2.569
Rv0950ko	-0.76	-2.053
Rv1096ko	-0.395	-0.648
Rv3684ko	-2.011	-1.87
delta_otsA_trehalose	1.757	2.222