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 Rv3188/-:

update plot	correlation	link to info on gene
Rv0691c/-	(cc=0.4375)	info on Rv0691c/-
Rv2800/-	(cc=0.4268)	info on Rv2800/-
Rv2310/-	(cc=0.424)	info on Rv2310/-
Rv0892/-	(cc=0.4136)	info on Rv0892/-
Rv1566c/-	(cc=0.4062)	info on Rv1566c/-
Rv2938/drrC	(cc=0.3902)	info on Rv2938/drrC
Rv2306B/-	(cc=0.3876)	info on Rv2306B/-
Rv1585c/-	(cc=0.384)	info on Rv1585c/-
Rv0798c/cfp29	(cc=0.3831)	info on Rv0798c/cfp29
Rv2957/-	(cc=0.3756)	info on Rv2957/-

Correlation of Rv3188/- with Rv2800/-

Normalized LFCs for Rv3188/-:
(description and provenance of datasets)

	Rv3188/-	Rv2800/-
Fe_supp_jason_reseq	0.395	-0.167
low_pH_jason_reseq	0.611	-0.545
NO_jason_reseq	-0.139	-0.236
B6_jason_reseq	0.151	0.485
MHCII_jason_reseq	1.439	0.614
Isoniazid02	-0.134	0.164
Rifampicin4	-0.677	0.55
Ethambutol3	-0.016	-0.216
Meropenem3	-0.031	0.079
Vancomycin16	-0.393	0.3
Rv2680_day32	-0.21	0.092
H37Rv_KO_MarP	0.12	0.236
hypoxia_3wks	0.223	0.363
hypoxia_6wks	-0.184	-0.367
glycerol	-0.518	0.424
cholesterol	0.268	0.064
AJ	0.38	0.136
Bibs02	-0.837	-0.668
Bibs02c	1.088	0.062
BL6	0.917	0.134
BL6a	0.915	-0.108
BXD01	0.476	-0.223
BXD010	0.255	-0.253
BXD011	0.443	-0.465
BXD03	0.683	0.464
BXD04	1.355	0.717
BXD05	-0.33	-0.041
BXD06	0.862	-0.182
BXD07	0.246	-0.097
BXD08	-0.415	0.279
BXD09	0.023	-0.179
CAST	-0.47	0.017
CCcont	0.93	-0.366
DS01	1.324	1.076
DS02	0.945	0.613
DS04	0.687	0.758
DS0c	0.52	0.946
GP01	-0.427	0.606
GP02	-1.837	-0.157
GP0c	-0.033	-0.211
NOD	2.211	2.379
NZO	-2.208	-0.172
PWK	-0.924	-0.185
H37Rv_KO_CtpC	0.515	-0.321
H37Rv_KO_CtpD	1.259	-0.462
H37Rv_KO_Rv1272	-0.288	-0.169
H37Rv_KO_SugABC	0.608	0.977
H37Rv_KO_MbtN	0.87	-0.754
Trans05	0.59	-0.212
macrophage_unactivated	2.058	2.108
IL1	0.332	-0.11
Rapamycin	0.055	-0.141
Tcell	-0.27	-0.502
GMCSF	-0.615	-0.048
IFNab	-0.426	0.242
IFNg	-1.264	-0.636
IFNg_GMCSF1	-0.352	0.085
Rv1432_day32	-0.961	0.19
Rv1565c_day32	-0.264	-0.071
secA2_input	0.141	-1.115
delta_Rv3594	-0.271	-0.35
delta_Rv3717	-0.035	0.015
delta_Rv3811	-0.87	-0.193
delta_Rv0954	-0.283	0.11
PonA1	-1.929	0.337
EccD1_KO	1.687	0.628
EspI_KO	0.074	0.302
PE35_KO	1.444	0.595
PPE68_KO	1.901	0.739
glycerol2	0.06	-0.436
lignocerate	0.789	-0.483
oleate	0.024	-0.098
phosphatidylcholine	0.584	-0.197
acetate	0.141	-0.057
glucAc	1.043	-0.52
Rv0950ko	-0.727	-0.485
Rv1096ko	0.555	0.323
Rv3684ko	0.082	-0.046
delta_otsA_trehalose	-1.196	-0.343