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 Rv2355/-

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

	Rv1424c/-	Rv2355/-
Fe_supp_jason_reseq	0.554	0.044
low_pH_jason_reseq	0.035	-0.564
NO_jason_reseq	0.108	0.158
B6_jason_reseq	0.256	-0.298
MHCII_jason_reseq	0.154	0.054
Isoniazid02	0.226	0.047
Rifampicin4	0.726	1.018
Ethambutol3	0.039	0.416
Meropenem3	0.255	-0.135
Vancomycin16	0.602	0.013
Rv2680_day32	-0.576	-0.084
H37Rv_KO_MarP	-0.044	-0.285
hypoxia_3wks	-0.722	0.419
hypoxia_6wks	0.777	0.125
glycerol	-0.434	-0.866
cholesterol	-0.054	-0.016
AJ	0.413	1.197
Bibs02	0.128	1.068
Bibs02c	0.373	1.675
BL6	-0.111	0.217
BL6a	0.528	1.072
BXD01	-0.36	0.643
BXD010	0.594	0.786
BXD011	0.784	0.752
BXD03	-0.231	0.715
BXD04	0.073	0.455
BXD05	0.281	0.947
BXD06	0.168	0.431
BXD07	-0.051	0.655
BXD08	0.574	0.538
BXD09	0.375	0.65
CAST	0.055	1.089
CCcont	-0.389	0.177
DS01	0.084	0.972
DS02	-0.027	1.007
DS04	0.915	1.317
DS0c	0.883	1.042
GP01	0.641	1.034
GP02	1.001	1.191
GP0c	0.672	0.53
NOD	0.054	1.318
NZO	0.532	0.984
PWK	0.31	1.098
H37Rv_KO_CtpC	0.753	0.752
H37Rv_KO_CtpD	0.728	0.953
H37Rv_KO_Rv1272	1.669	0.57
H37Rv_KO_SugABC	1.084	1.016
H37Rv_KO_MbtN	0.682	0.685
Trans05	0.714	0.851
macrophage_unactivated	0.0	-0.59
IL1	-0.629	-0.306
Rapamycin	0.531	-0.335
Tcell	-0.355	-1.017
GMCSF	0.169	-0.272
IFNab	-0.46	-0.729
IFNg	1.066	-0.428
IFNg_GMCSF1	0.0	-0.226
Rv1432_day32	1.701	0.492
Rv1565c_day32	0.782	0.278
secA2_input	1.071	-0.315
delta_Rv3594	0.408	-0.153
delta_Rv3717	0.239	-0.344
delta_Rv3811	0.253	-0.116
delta_Rv0954	0.27	0.429
PonA1	0.173	0.0
EccD1_KO	0.395	0.214
EspI_KO	1.184	0.676
PE35_KO	1.345	0.79
PPE68_KO	1.123	0.464
glycerol2	-0.789	-0.787
lignocerate	-0.66	-0.553
oleate	-0.196	-0.871
phosphatidylcholine	-0.508	-0.774
acetate	-1.122	-0.321
glucAc	-0.931	-0.055
Rv0950ko	-0.703	0.166
Rv1096ko	-0.703	-0.018
Rv3684ko	-0.963	-0.38
delta_otsA_trehalose	-0.303	-0.173