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 Rv3312A/-:

update plot	correlation	link to info on gene
Rv1680/-	(cc=0.5035)	info on Rv1680/-
Rv3691/-	(cc=0.4858)	info on Rv3691/-
Rv3703c/-	(cc=0.4702)	info on Rv3703c/-
Rv3395c/-	(cc=0.4565)	info on Rv3395c/-
Rv3256c/-	(cc=0.4528)	info on Rv3256c/-
Rv3836/-	(cc=0.4501)	info on Rv3836/-
Rv2404c/lepA	(cc=0.447)	info on Rv2404c/lepA
Rv2583c/relA	(cc=0.4342)	info on Rv2583c/relA
Rv1569/bioF1	(cc=0.4332)	info on Rv1569/bioF1
Rv1558/-	(cc=0.4323)	info on Rv1558/-

Correlation of Rv3312A/- with Rv1558/-

Normalized LFCs for Rv3312A/-:
(description and provenance of datasets)

	Rv3312A/-	Rv1558/-
Fe_supp_jason_reseq	-0.35	0.248
low_pH_jason_reseq	-0.132	-1.022
NO_jason_reseq	0.893	0.058
B6_jason_reseq	1.266	0.883
MHCII_jason_reseq	0.295	1.104
Isoniazid02	0.941	-0.687
Rifampicin4	0.742	0.682
Ethambutol3	0.548	-0.305
Meropenem3	2.13	1.242
Vancomycin16	0.727	-0.159
Rv2680_day32	-0.959	0.042
H37Rv_KO_MarP	0.344	0.144
hypoxia_3wks	-0.231	-0.287
hypoxia_6wks	-0.395	-0.507
glycerol	0.726	-0.503
cholesterol	0.382	-0.504
AJ	0.225	0.462
Bibs02	-1.288	0.487
Bibs02c	-0.975	0.649
BL6	-0.038	-0.091
BL6a	-0.436	0.317
BXD01	0.434	-0.044
BXD010	-0.436	0.523
BXD011	-0.098	0.149
BXD03	0.181	0.256
BXD04	-0.474	0.326
BXD05	0.265	-0.067
BXD06	0.331	0.24
BXD07	0.75	0.107
BXD08	-0.034	0.218
BXD09	0.066	0.189
CAST	-0.017	0.023
CCcont	0.157	-0.421
DS01	-0.27	0.645
DS02	0.274	0.501
DS04	0.022	0.479
DS0c	0.064	1.358
GP01	0.31	0.343
GP02	1.1	0.554
GP0c	0.597	-0.201
NOD	0.382	-0.436
NZO	-0.377	0.462
PWK	-0.328	0.311
H37Rv_KO_CtpC	-0.717	0.312
H37Rv_KO_CtpD	0.144	0.568
H37Rv_KO_Rv1272	-0.912	-1.188
H37Rv_KO_SugABC	-0.312	-1.189
H37Rv_KO_MbtN	0.777	0.35
Trans05	-0.372	-0.949
macrophage_unactivated	0.133	0.098
IL1	0.113	0.409
Rapamycin	0.292	0.543
Tcell	0.336	0.186
GMCSF	-0.034	0.399
IFNab	-0.804	-0.269
IFNg	0.551	0.123
IFNg_GMCSF1	-0.478	0.135
Rv1432_day32	0.48	-0.623
Rv1565c_day32	-3.838	-3.116
secA2_input	0.243	-0.122
delta_Rv3594	1.41	-0.099
delta_Rv3717	1.221	-0.186
delta_Rv3811	0.55	-0.335
delta_Rv0954	1.469	0.647
PonA1	1.13	0.9
EccD1_KO	-0.747	-0.585
EspI_KO	-0.374	0.348
PE35_KO	-0.875	0.292
PPE68_KO	-0.771	0.87
glycerol2	1.241	0.397
lignocerate	1.444	0.385
oleate	0.771	0.72
phosphatidylcholine	1.408	0.469
acetate	0.48	-0.336
glucAc	0.764	0.241
Rv0950ko	0.519	0.552
Rv1096ko	0.452	-0.181
Rv3684ko	0.252	0.095
delta_otsA_trehalose	-0.354	1.305