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 Rv1424c/-:

update plot	correlation	link to info on gene
Rv2083/-	(cc=0.5161)	info on Rv2083/-
Rv0011c/-	(cc=0.5133)	info on Rv0011c/-
Rv2136c/-	(cc=0.5107)	info on Rv2136c/-
Rv3475/-	(cc=0.4888)	info on Rv3475/-
Rv3022A/PE29	(cc=0.4808)	info on Rv3022A/PE29
Rv2355/-	(cc=0.4798)	info on Rv2355/-
Rv2270/lppN	(cc=0.4734)	info on Rv2270/lppN
Rv1554/frdC	(cc=0.4731)	info on Rv1554/frdC
Rv1984c/cfp21	(cc=0.4666)	info on Rv1984c/cfp21
Rv2649/-	(cc=0.4647)	info on Rv2649/-

Correlation of Rv1424c/- with Rv2083/-

Normalized LFCs for Rv1424c/-:
(description and provenance of datasets)

	Rv1424c/-	Rv2083/-
Fe_supp_jason_reseq	0.554	0.221
low_pH_jason_reseq	0.035	0.843
NO_jason_reseq	0.108	-0.782
B6_jason_reseq	0.256	-0.223
MHCII_jason_reseq	0.154	0.977
Isoniazid02	0.226	0.64
Rifampicin4	0.726	1.324
Ethambutol3	0.039	2.234
Meropenem3	0.255	0.758
Vancomycin16	0.602	0.499
Rv2680_day32	-0.576	0.184
H37Rv_KO_MarP	-0.044	-0.217
hypoxia_3wks	-0.722	0.53
hypoxia_6wks	0.777	-0.215
glycerol	-0.434	0.613
cholesterol	-0.054	0.119
AJ	0.413	0.829
Bibs02	0.128	0.27
Bibs02c	0.373	1.643
BL6	-0.111	-0.434
BL6a	0.528	1.247
BXD01	-0.36	-0.269
BXD010	0.594	0.488
BXD011	0.784	-0.09
BXD03	-0.231	0.594
BXD04	0.073	0.294
BXD05	0.281	0.045
BXD06	0.168	-0.221
BXD07	-0.051	-0.458
BXD08	0.574	0.116
BXD09	0.375	0.365
CAST	0.055	0.527
CCcont	-0.389	-0.817
DS01	0.084	1.304
DS02	-0.027	0.632
DS04	0.915	0.371
DS0c	0.883	-0.127
GP01	0.641	0.039
GP02	1.001	1.442
GP0c	0.672	0.378
NOD	0.054	0.574
NZO	0.532	0.688
PWK	0.31	0.709
H37Rv_KO_CtpC	0.753	1.012
H37Rv_KO_CtpD	0.728	0.686
H37Rv_KO_Rv1272	1.669	1.624
H37Rv_KO_SugABC	1.084	0.703
H37Rv_KO_MbtN	0.682	-0.832
Trans05	0.714	0.935
macrophage_unactivated	0.0	0.83
IL1	-0.629	0.952
Rapamycin	0.531	0.147
Tcell	-0.355	0.137
GMCSF	0.169	0.473
IFNab	-0.46	1.052
IFNg	1.066	1.229
IFNg_GMCSF1	0.0	0.581
Rv1432_day32	1.701	0.777
Rv1565c_day32	0.782	0.584
secA2_input	1.071	0.205
delta_Rv3594	0.408	0.662
delta_Rv3717	0.239	0.94
delta_Rv3811	0.253	0.956
delta_Rv0954	0.27	0.804
PonA1	0.173	-0.882
EccD1_KO	0.395	1.184
EspI_KO	1.184	1.363
PE35_KO	1.345	0.974
PPE68_KO	1.123	0.336
glycerol2	-0.789	-0.921
lignocerate	-0.66	-1.23
oleate	-0.196	-0.037
phosphatidylcholine	-0.508	-0.534
acetate	-1.122	-1.769
glucAc	-0.931	-2.327
Rv0950ko	-0.703	-0.748
Rv1096ko	-0.703	-0.679
Rv3684ko	-0.963	-1.461
delta_otsA_trehalose	-0.303	1.124