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 Rv1639c/-:

update plot	correlation	link to info on gene
Rv2119/-	(cc=0.5287)	info on Rv2119/-
Rv0278c/PE_PGRS3	(cc=0.5277)	info on Rv0278c/PE_PGRS3
Rv2019/-	(cc=0.5176)	info on Rv2019/-
Rv1139c/-	(cc=0.4907)	info on Rv1139c/-
Rv2819c/-	(cc=0.4887)	info on Rv2819c/-
Rv0794c/-	(cc=0.4695)	info on Rv0794c/-
Rv0084/hycD	(cc=0.453)	info on Rv0084/hycD
Rv2396/PE_PGRS41	(cc=0.4526)	info on Rv2396/PE_PGRS41
Rv1352/-	(cc=0.4373)	info on Rv1352/-
Rv0771/-	(cc=0.4336)	info on Rv0771/-

Correlation of Rv1639c/- with Rv2119/-

Normalized LFCs for Rv1639c/-:
(description and provenance of datasets)

	Rv1639c/-	Rv2119/-
Fe_supp_jason_reseq	0.646	0.362
low_pH_jason_reseq	-0.93	-0.837
NO_jason_reseq	-0.249	0.16
B6_jason_reseq	0.012	0.739
MHCII_jason_reseq	0.966	0.235
Isoniazid02	0.041	-0.028
Rifampicin4	0.468	0.176
Ethambutol3	0.017	-0.083
Meropenem3	-0.217	-0.787
Vancomycin16	0.146	-0.024
Rv2680_day32	0.579	-0.497
H37Rv_KO_MarP	0.052	-0.12
hypoxia_3wks	-0.574	-0.774
hypoxia_6wks	0.403	0.236
glycerol	0.418	0.155
cholesterol	0.067	-0.227
AJ	0.336	0.034
Bibs02	0.543	-0.498
Bibs02c	-0.402	-0.629
BL6	-0.24	0.572
BL6a	0.013	-0.133
BXD01	0.765	-0.109
BXD010	-0.136	0.182
BXD011	0.352	0.14
BXD03	-0.195	0.573
BXD04	0.221	0.288
BXD05	0.071	0.139
BXD06	0.154	0.231
BXD07	0.59	0.171
BXD08	-0.073	0.564
BXD09	-0.4	0.031
CAST	-0.719	-0.379
CCcont	-0.204	0.357
DS01	0.031	0.38
DS02	-0.12	-0.096
DS04	-0.372	0.042
DS0c	0.611	0.349
GP01	-0.166	-0.26
GP02	0.186	-0.018
GP0c	-0.68	-0.33
NOD	-0.892	-0.117
NZO	-0.168	-0.029
PWK	0.385	-0.072
H37Rv_KO_CtpC	-0.011	0.0
H37Rv_KO_CtpD	0.115	0.481
H37Rv_KO_Rv1272	0.047	-0.479
H37Rv_KO_SugABC	-0.256	0.457
H37Rv_KO_MbtN	0.367	0.252
Trans05	0.077	-0.54
macrophage_unactivated	-0.638	0.069
IL1	-0.543	-0.75
Rapamycin	0.546	-0.672
Tcell	0.137	0.701
GMCSF	-0.43	0.383
IFNab	-0.184	-0.686
IFNg	-0.024	-0.607
IFNg_GMCSF1	0.082	-1.046
Rv1432_day32	0.108	-0.282
Rv1565c_day32	-0.693	-0.158
secA2_input	-0.321	-0.698
delta_Rv3594	0.11	-0.259
delta_Rv3717	-0.255	-0.293
delta_Rv3811	-0.266	-0.085
delta_Rv0954	-1.39	-0.274
PonA1	0.269	-0.171
EccD1_KO	0.141	0.559
EspI_KO	0.545	0.0
PE35_KO	0.703	0.831
PPE68_KO	1.731	0.973
glycerol2	0.904	0.874
lignocerate	1.439	0.997
oleate	0.588	-0.147
phosphatidylcholine	0.803	0.856
acetate	1.225	1.839
glucAc	0.739	1.391
Rv0950ko	-0.675	-0.154
Rv1096ko	0.353	-0.311
Rv3684ko	-0.121	-0.337
delta_otsA_trehalose	-0.439	-0.682