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 Rv3022A/PE29:

update plot	correlation	link to info on gene
Rv2543/lppA	(cc=0.5866)	info on Rv2543/lppA
Rv1396c/PE_PGRS25	(cc=0.548)	info on Rv1396c/PE_PGRS25
Rv0526/-	(cc=0.5258)	info on Rv0526/-
Rv2519/PE26	(cc=0.5243)	info on Rv2519/PE26
Rv1173/fbiC	(cc=0.5135)	info on Rv1173/fbiC
Rv2807/-	(cc=0.5131)	info on Rv2807/-
Rv1067c/PE_PGRS19	(cc=0.5123)	info on Rv1067c/PE_PGRS19
Rv1918c/PPE35	(cc=0.5079)	info on Rv1918c/PPE35
Rv3023c/-	(cc=0.5041)	info on Rv3023c/-
Rv1047/-	(cc=0.5)	info on Rv1047/-

Correlation of Rv3022A/PE29 with Rv2519/PE26

Normalized LFCs for Rv3022A/PE29:
(description and provenance of datasets)

	Rv3022A/PE29	Rv2519/PE26
Fe_supp_jason_reseq	0.275	0.458
low_pH_jason_reseq	-0.381	-0.074
NO_jason_reseq	-0.709	0.045
B6_jason_reseq	-0.585	-0.416
MHCII_jason_reseq	-0.709	-0.542
Isoniazid02	0.994	0.412
Rifampicin4	0.967	0.387
Ethambutol3	0.434	1.008
Meropenem3	0.291	0.339
Vancomycin16	0.594	0.329
Rv2680_day32	-0.826	0.166
H37Rv_KO_MarP	0.165	0.147
hypoxia_3wks	0.347	-0.211
hypoxia_6wks	-0.81	-0.271
glycerol	0.73	0.118
cholesterol	1.146	0.45
AJ	2.274	-0.047
Bibs02	0.167	0.054
Bibs02c	0.893	0.22
BL6	0.569	0.795
BL6a	0.641	0.446
BXD01	0.898	0.534
BXD010	0.456	0.61
BXD011	0.286	0.328
BXD03	0.216	0.626
BXD04	0.063	0.605
BXD05	0.775	0.477
BXD06	0.593	0.848
BXD07	0.93	0.255
BXD08	0.28	0.667
BXD09	0.383	0.427
CAST	1.099	0.22
CCcont	1.022	0.582
DS01	0.883	0.414
DS02	0.745	0.577
DS04	0.748	0.898
DS0c	-0.019	0.189
GP01	0.72	0.489
GP02	0.311	0.524
GP0c	0.208	0.489
NOD	0.919	-0.14
NZO	-0.088	0.559
PWK	0.494	-0.32
H37Rv_KO_CtpC	1.553	1.638
H37Rv_KO_CtpD	1.287	1.208
H37Rv_KO_Rv1272	2.221	1.124
H37Rv_KO_SugABC	0.898	1.198
H37Rv_KO_MbtN	0.687	0.878
Trans05	1.378	1.06
macrophage_unactivated	0.767	0.527
IL1	0.039	0.225
Rapamycin	0.264	0.068
Tcell	0.525	0.072
GMCSF	1.333	0.441
IFNab	0.768	-0.172
IFNg	0.083	-0.278
IFNg_GMCSF1	0.289	0.204
Rv1432_day32	0.85	0.029
Rv1565c_day32	2.139	0.43
secA2_input	0.182	-0.495
delta_Rv3594	0.34	-0.09
delta_Rv3717	0.145	0.26
delta_Rv3811	0.427	0.126
delta_Rv0954	-0.225	0.202
PonA1	0.516	0.129
EccD1_KO	0.947	-0.184
EspI_KO	1.178	0.0
PE35_KO	0.84	-0.082
PPE68_KO	0.579	-0.525
glycerol2	-1.302	-0.468
lignocerate	-0.961	-0.16
oleate	-1.032	-0.885
phosphatidylcholine	-0.819	-0.109
acetate	-1.248	-0.721
glucAc	-0.722	-0.159
Rv0950ko	0.555	-0.096
Rv1096ko	-0.347	-0.618
Rv3684ko	-0.354	-0.524
delta_otsA_trehalose	-1.531	0.519