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 Rv1904/-:

update plot	correlation	link to info on gene
Rv3767c/-	(cc=0.4995)	info on Rv3767c/-
Rv2268c/cyp128	(cc=0.4679)	info on Rv2268c/cyp128
Rv0338c/-	(cc=0.4656)	info on Rv0338c/-
Rv2443/dctA	(cc=0.4579)	info on Rv2443/dctA
Rv1372/-	(cc=0.4402)	info on Rv1372/-
Rv1770/-	(cc=0.4373)	info on Rv1770/-
Rv0320/-	(cc=0.436)	info on Rv0320/-
Rv3839/-	(cc=0.431)	info on Rv3839/-
Rv2090/-	(cc=0.4169)	info on Rv2090/-
Rv2431c/PE25	(cc=0.4042)	info on Rv2431c/PE25

Correlation of Rv1904/- with Rv1372/-

Normalized LFCs for Rv1904/-:
(description and provenance of datasets)

	Rv1904/-	Rv1372/-
Fe_supp_jason_reseq	-0.229	0.878
low_pH_jason_reseq	-0.962	-0.356
NO_jason_reseq	-0.675	-0.076
B6_jason_reseq	-0.878	-0.273
MHCII_jason_reseq	-0.527	0.298
Isoniazid02	-0.476	-0.038
Rifampicin4	-0.19	-0.615
Ethambutol3	-0.139	-0.098
Meropenem3	-0.285	-0.425
Vancomycin16	-0.491	0.138
Rv2680_day32	0.919	0.228
H37Rv_KO_MarP	0.097	0.121
hypoxia_3wks	0.195	-0.227
hypoxia_6wks	-0.09	-1.027
glycerol	0.336	-0.31
cholesterol	2.757	1.593
AJ	0.736	0.054
Bibs02	0.254	-0.331
Bibs02c	-0.12	0.677
BL6	0.867	0.814
BL6a	0.451	1.363
BXD01	0.113	1.566
BXD010	-0.15	1.45
BXD011	0.31	1.01
BXD03	0.358	1.073
BXD04	0.133	2.511
BXD05	0.481	1.263
BXD06	0.367	1.226
BXD07	0.549	0.987
BXD08	-0.413	1.274
BXD09	0.478	0.841
CAST	0.355	0.939
CCcont	-0.517	0.894
DS01	-0.034	0.055
DS02	0.555	-0.723
DS04	-0.687	0.628
DS0c	-0.077	0.379
GP01	0.336	1.245
GP02	0.741	1.917
GP0c	-0.042	1.142
NOD	0.952	1.573
NZO	0.572	0.646
PWK	0.399	0.601
H37Rv_KO_CtpC	0.487	0.859
H37Rv_KO_CtpD	0.476	0.67
H37Rv_KO_Rv1272	0.993	1.429
H37Rv_KO_SugABC	-0.662	-1.114
H37Rv_KO_MbtN	0.325	-0.609
Trans05	0.138	0.0
macrophage_unactivated	0.335	0.467
IL1	-0.214	-0.489
Rapamycin	0.381	0.117
Tcell	0.163	0.867
GMCSF	0.689	-0.267
IFNab	0.012	-1.539
IFNg	0.361	0.347
IFNg_GMCSF1	0.6	0.786
Rv1432_day32	0.321	-1.276
Rv1565c_day32	0.145	0.706
secA2_input	-0.352	-1.722
delta_Rv3594	-0.531	0.748
delta_Rv3717	-0.122	0.0
delta_Rv3811	-0.22	-0.407
delta_Rv0954	-0.771	-1.088
PonA1	0.067	0.717
EccD1_KO	-0.059	-0.214
EspI_KO	0.362	-0.123
PE35_KO	-0.321	-0.061
PPE68_KO	-1.005	0.198
glycerol2	-0.21	-0.357
lignocerate	-0.242	-0.585
oleate	0.102	-0.035
phosphatidylcholine	-0.22	-0.048
acetate	-0.342	-1.001
glucAc	-0.079	-0.975
Rv0950ko	0.7	-0.398
Rv1096ko	-0.802	-1.252
Rv3684ko	-0.691	-0.242
delta_otsA_trehalose	2.548	1.429