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 Rv3404c/-:

update plot	correlation	link to info on gene
Rv2443/dctA	(cc=0.51)	info on Rv2443/dctA
Rv0073/-	(cc=0.5038)	info on Rv0073/-
Rv2705c/-	(cc=0.4841)	info on Rv2705c/-
Rv0403c/mmpS1	(cc=0.454)	info on Rv0403c/mmpS1
Rv0404/fadD30	(cc=0.4502)	info on Rv0404/fadD30
Rv2431c/PE25	(cc=0.4431)	info on Rv2431c/PE25
Rv1949c/-	(cc=0.424)	info on Rv1949c/-
Rv0148/-	(cc=0.4119)	info on Rv0148/-
Rv1904/-	(cc=0.3998)	info on Rv1904/-
Rv0144/-	(cc=0.399)	info on Rv0144/-

Correlation of Rv3404c/- with Rv2443/dctA

Normalized LFCs for Rv3404c/-:
(description and provenance of datasets)

	Rv3404c/-	Rv2443/dctA
Fe_supp_jason_reseq	-0.442	-0.074
low_pH_jason_reseq	0.701	-1.052
NO_jason_reseq	0.024	-0.108
B6_jason_reseq	-0.342	-0.548
MHCII_jason_reseq	-0.684	-0.268
Isoniazid02	-0.435	-0.426
Rifampicin4	-0.542	0.049
Ethambutol3	0.015	-0.383
Meropenem3	-0.448	0.152
Vancomycin16	-0.793	-0.501
Rv2680_day32	0.336	0.053
H37Rv_KO_MarP	0.483	-0.121
hypoxia_3wks	0.606	-0.068
hypoxia_6wks	0.109	0.267
glycerol	0.038	-0.601
cholesterol	0.055	0.37
AJ	0.672	0.977
Bibs02	0.421	0.424
Bibs02c	0.327	-0.238
BL6	-0.242	0.607
BL6a	0.277	0.026
BXD01	0.276	0.443
BXD010	0.166	0.305
BXD011	0.152	0.372
BXD03	0.631	0.386
BXD04	0.285	0.409
BXD05	0.451	0.023
BXD06	0.099	0.535
BXD07	-0.194	0.444
BXD08	-0.27	0.468
BXD09	0.073	0.321
CAST	-0.137	0.469
CCcont	-0.688	-0.236
DS01	0.506	0.224
DS02	0.999	0.224
DS04	0.073	0.707
DS0c	0.841	0.127
GP01	-0.169	0.029
GP02	0.508	1.221
GP0c	-0.546	-0.023
NOD	0.722	0.926
NZO	0.566	0.433
PWK	0.885	1.698
H37Rv_KO_CtpC	-0.013	0.021
H37Rv_KO_CtpD	0.713	0.851
H37Rv_KO_Rv1272	0.781	0.262
H37Rv_KO_SugABC	0.184	0.711
H37Rv_KO_MbtN	-0.771	0.026
Trans05	0.864	-0.081
macrophage_unactivated	0.401	0.347
IL1	-0.555	-0.492
Rapamycin	0.267	-0.488
Tcell	0.137	-0.14
GMCSF	0.243	0.127
IFNab	-0.42	-0.166
IFNg	0.339	0.556
IFNg_GMCSF1	-0.17	0.892
Rv1432_day32	0.381	0.262
Rv1565c_day32	0.798	0.889
secA2_input	-1.118	-0.728
delta_Rv3594	-0.433	-0.486
delta_Rv3717	-0.391	-0.79
delta_Rv3811	0.452	-0.431
delta_Rv0954	-0.127	0.481
PonA1	-0.047	0.369
EccD1_KO	-0.243	-0.332
EspI_KO	0.023	-0.599
PE35_KO	-0.429	-0.551
PPE68_KO	-0.614	-0.787
glycerol2	0.502	0.067
lignocerate	-0.23	-0.03
oleate	1.259	0.492
phosphatidylcholine	0.657	0.242
acetate	-0.826	-0.258
glucAc	-1.839	-0.762
Rv0950ko	0.386	-0.25
Rv1096ko	-0.344	-0.835
Rv3684ko	-0.147	-0.698
delta_otsA_trehalose	0.898	0.483