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 Rv2896c/-:

update plot	correlation	link to info on gene
Rv1961/-	(cc=0.4625)	info on Rv1961/-
Rv0976c/-	(cc=0.4607)	info on Rv0976c/-
Rv2159c/-	(cc=0.4461)	info on Rv2159c/-
Rv3292/-	(cc=0.446)	info on Rv3292/-
Rv2012/-	(cc=0.426)	info on Rv2012/-
Rv0897c/-	(cc=0.4057)	info on Rv0897c/-
Rv0992c/-	(cc=0.404)	info on Rv0992c/-
Rv0994/moeA1	(cc=0.4033)	info on Rv0994/moeA1
Rv1452c/PE_PGRS28	(cc=0.3929)	info on Rv1452c/PE_PGRS28
Rv0222/echA1	(cc=0.3881)	info on Rv0222/echA1

Correlation of Rv2896c/- with Rv1961/-

Normalized LFCs for Rv2896c/-:
(description and provenance of datasets)

	Rv2896c/-	Rv1961/-
Fe_supp_jason_reseq	-0.685	-2.406
low_pH_jason_reseq	-0.932	-2.08
NO_jason_reseq	0.263	0.184
B6_jason_reseq	-0.482	-1.989
MHCII_jason_reseq	-0.754	-1.677
Isoniazid02	0.764	0.236
Rifampicin4	-0.181	-0.06
Ethambutol3	0.188	-0.407
Meropenem3	0.114	-0.386
Vancomycin16	0.058	-0.114
Rv2680_day32	-0.456	-1.231
H37Rv_KO_MarP	-0.051	-0.188
hypoxia_3wks	-0.287	-0.929
hypoxia_6wks	-0.624	-0.411
glycerol	1.546	0.13
cholesterol	0.503	-0.233
AJ	-0.128	0.533
Bibs02	0.654	0.242
Bibs02c	-0.115	-0.399
BL6	0.637	0.758
BL6a	0.103	-0.118
BXD01	-0.299	-0.901
BXD010	-0.223	-0.906
BXD011	-0.269	-0.524
BXD03	-0.562	-0.369
BXD04	0.256	-0.494
BXD05	0.261	0.076
BXD06	-0.173	-0.241
BXD07	0.082	0.272
BXD08	0.117	0.156
BXD09	-0.182	-0.147
CAST	-0.108	0.287
CCcont	-0.035	-0.33
DS01	0.674	0.527
DS02	0.767	0.158
DS04	0.706	0.843
DS0c	0.607	-0.789
GP01	0.022	0.532
GP02	0.98	1.445
GP0c	0.465	1.337
NOD	0.792	-0.496
NZO	-0.078	0.92
PWK	-0.413	-1.091
H37Rv_KO_CtpC	0.386	0.04
H37Rv_KO_CtpD	0.78	-0.241
H37Rv_KO_Rv1272	-0.435	-0.254
H37Rv_KO_SugABC	-1.474	0.123
H37Rv_KO_MbtN	0.529	-0.052
Trans05	-0.377	-0.223
macrophage_unactivated	0.18	-1.225
IL1	0.516	-0.219
Rapamycin	0.206	0.031
Tcell	-0.329	-0.277
GMCSF	-0.351	0.264
IFNab	-0.121	0.184
IFNg	0.489	-0.377
IFNg_GMCSF1	0.179	0.063
Rv1432_day32	0.738	0.331
Rv1565c_day32	0.491	-0.595
secA2_input	0.435	0.13
delta_Rv3594	-0.286	0.171
delta_Rv3717	0.083	0.858
delta_Rv3811	0.0	1.316
delta_Rv0954	-0.261	0.51
PonA1	-0.485	-0.609
EccD1_KO	-0.145	-0.158
EspI_KO	-0.083	-0.511
PE35_KO	0.545	-0.618
PPE68_KO	0.518	-0.154
glycerol2	-0.303	-0.118
lignocerate	0.558	0.587
oleate	-0.072	-1.456
phosphatidylcholine	0.31	0.182
acetate	0.472	1.076
glucAc	0.304	1.194
Rv0950ko	0.172	0.917
Rv1096ko	0.829	0.66
Rv3684ko	0.576	0.357
delta_otsA_trehalose	-0.416	-0.152