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 Rv0338c/-

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

	Rv1904/-	Rv0338c/-
Fe_supp_jason_reseq	-0.229	0.0
low_pH_jason_reseq	-0.962	0.0
NO_jason_reseq	-0.675	0.0
B6_jason_reseq	-0.878	0.0
MHCII_jason_reseq	-0.527	0.0
Isoniazid02	-0.476	0.0
Rifampicin4	-0.19	0.0
Ethambutol3	-0.139	0.0
Meropenem3	-0.285	0.0
Vancomycin16	-0.491	0.0
Rv2680_day32	0.919	0.0
H37Rv_KO_MarP	0.097	0.0
hypoxia_3wks	0.195	0.0
hypoxia_6wks	-0.09	0.0
glycerol	0.336	0.385
cholesterol	2.757	3.545
AJ	0.736	0.0
Bibs02	0.254	0.0
Bibs02c	-0.12	0.0
BL6	0.867	0.0
BL6a	0.451	0.0
BXD01	0.113	0.0
BXD010	-0.15	0.0
BXD011	0.31	0.0
BXD03	0.358	0.0
BXD04	0.133	0.0
BXD05	0.481	0.0
BXD06	0.367	0.0
BXD07	0.549	0.0
BXD08	-0.413	0.0
BXD09	0.478	0.0
CAST	0.355	0.0
CCcont	-0.517	0.0
DS01	-0.034	0.0
DS02	0.555	0.0
DS04	-0.687	0.0
DS0c	-0.077	0.0
GP01	0.336	0.0
GP02	0.741	0.0
GP0c	-0.042	0.0
NOD	0.952	0.0
NZO	0.572	0.0
PWK	0.399	0.0
H37Rv_KO_CtpC	0.487	0.0
H37Rv_KO_CtpD	0.476	0.0
H37Rv_KO_Rv1272	0.993	0.0
H37Rv_KO_SugABC	-0.662	0.0
H37Rv_KO_MbtN	0.325	0.0
Trans05	0.138	0.0
macrophage_unactivated	0.335	0.0
IL1	-0.214	0.0
Rapamycin	0.381	0.0
Tcell	0.163	0.0
GMCSF	0.689	0.0
IFNab	0.012	0.0
IFNg	0.361	0.0
IFNg_GMCSF1	0.6	0.0
Rv1432_day32	0.321	0.0
Rv1565c_day32	0.145	0.0
secA2_input	-0.352	0.847
delta_Rv3594	-0.531	0.0
delta_Rv3717	-0.122	0.0
delta_Rv3811	-0.22	0.0
delta_Rv0954	-0.771	0.0
PonA1	0.067	0.0
EccD1_KO	-0.059	0.0
EspI_KO	0.362	0.0
PE35_KO	-0.321	0.0
PPE68_KO	-1.005	0.0
glycerol2	-0.21	0.0
lignocerate	-0.242	0.0
oleate	0.102	0.0
phosphatidylcholine	-0.22	0.0
acetate	-0.342	0.0
glucAc	-0.079	0.0
Rv0950ko	0.7	0.0
Rv1096ko	-0.802	0.0
Rv3684ko	-0.691	0.0
delta_otsA_trehalose	2.548	0.133