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 Rv1498c/-:

update plot	correlation	link to info on gene
Rv2775/-	(cc=0.6072)	info on Rv2775/-
Rv0940c/-	(cc=0.5976)	info on Rv0940c/-
Rv0932c/pstS2	(cc=0.5937)	info on Rv0932c/pstS2
Rv2452c/-	(cc=0.584)	info on Rv2452c/-
Rv2957/-	(cc=0.5722)	info on Rv2957/-
Rv1896c/-	(cc=0.5617)	info on Rv1896c/-
Rv2275/-	(cc=0.5612)	info on Rv2275/-
Rv3397c/phyA	(cc=0.5581)	info on Rv3397c/phyA
Rv2816c/-	(cc=0.5533)	info on Rv2816c/-
Rv1501/-	(cc=0.5387)	info on Rv1501/-

Correlation of Rv1498c/- with Rv2775/-

Normalized LFCs for Rv1498c/-:
(description and provenance of datasets)

	Rv1498c/-	Rv2775/-
Fe_supp_jason_reseq	1.557	0.466
low_pH_jason_reseq	0.499	-0.037
NO_jason_reseq	0.339	-0.977
B6_jason_reseq	-0.235	0.469
MHCII_jason_reseq	-0.081	-0.364
Isoniazid02	-1.26	-0.389
Rifampicin4	0.23	-0.038
Ethambutol3	-1.16	-0.276
Meropenem3	-1.318	-1.548
Vancomycin16	-0.806	-0.127
Rv2680_day32	0.016	-0.205
H37Rv_KO_MarP	-0.631	-0.666
hypoxia_3wks	0.443	-0.817
hypoxia_6wks	0.092	0.058
glycerol	-0.064	-1.814
cholesterol	0.441	-1.544
AJ	0.402	0.474
Bibs02	0.525	-1.113
Bibs02c	-0.189	-0.1
BL6	0.969	0.246
BL6a	0.65	0.595
BXD01	0.548	0.083
BXD010	1.26	1.009
BXD011	1.351	0.952
BXD03	0.869	0.569
BXD04	0.713	0.432
BXD05	1.417	2.161
BXD06	0.962	1.25
BXD07	0.97	0.675
BXD08	0.654	0.499
BXD09	0.855	0.951
CAST	-0.35	0.592
CCcont	0.82	0.59
DS01	0.517	0.994
DS02	-0.391	-0.378
DS04	0.817	0.037
DS0c	0.434	-0.192
GP01	0.704	1.913
GP02	0.51	0.55
GP0c	0.225	1.296
NOD	1.538	1.394
NZO	0.548	0.162
PWK	0.644	1.047
H37Rv_KO_CtpC	1.414	0.599
H37Rv_KO_CtpD	0.01	1.142
H37Rv_KO_Rv1272	0.942	1.787
H37Rv_KO_SugABC	1.369	1.287
H37Rv_KO_MbtN	0.905	0.538
Trans05	1.564	1.467
macrophage_unactivated	0.404	0.524
IL1	0.08	-0.35
Rapamycin	0.015	0.964
Tcell	0.384	-0.775
GMCSF	-0.071	0.525
IFNab	0.082	0.747
IFNg	0.633	0.083
IFNg_GMCSF1	0.54	0.019
Rv1432_day32	0.282	0.113
Rv1565c_day32	0.646	0.199
secA2_input	-0.233	0.172
delta_Rv3594	-0.205	-0.812
delta_Rv3717	-0.238	-1.117
delta_Rv3811	-0.691	-1.056
delta_Rv0954	-0.702	-1.181
PonA1	-0.268	-2.209
EccD1_KO	0.865	0.506
EspI_KO	0.85	1.269
PE35_KO	1.397	1.502
PPE68_KO	1.667	1.574
glycerol2	0.252	0.0
lignocerate	0.818	0.935
oleate	0.109	-1.208
phosphatidylcholine	0.374	0.629
acetate	0.332	0.469
glucAc	0.76	0.563
Rv0950ko	0.241	0.389
Rv1096ko	-0.908	0.178
Rv3684ko	-0.301	-0.098
delta_otsA_trehalose	-1.361	-0.085