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 Rv1067c/PE_PGRS19

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

	Rv3022A/PE29	Rv1067c/PE_PGRS19
Fe_supp_jason_reseq	0.275	0.137
low_pH_jason_reseq	-0.381	-0.734
NO_jason_reseq	-0.709	-0.559
B6_jason_reseq	-0.585	-0.082
MHCII_jason_reseq	-0.709	-0.054
Isoniazid02	0.994	-0.706
Rifampicin4	0.967	-0.087
Ethambutol3	0.434	-0.019
Meropenem3	0.291	1.429
Vancomycin16	0.594	-0.589
Rv2680_day32	-0.826	-0.223
H37Rv_KO_MarP	0.165	-0.133
hypoxia_3wks	0.347	-0.056
hypoxia_6wks	-0.81	-0.589
glycerol	0.73	1.303
cholesterol	1.146	0.513
AJ	2.274	1.277
Bibs02	0.167	0.313
Bibs02c	0.893	0.474
BL6	0.569	-0.18
BL6a	0.641	-0.174
BXD01	0.898	0.78
BXD010	0.456	0.104
BXD011	0.286	-0.313
BXD03	0.216	-0.046
BXD04	0.063	-0.178
BXD05	0.775	-0.22
BXD06	0.593	0.407
BXD07	0.93	0.068
BXD08	0.28	0.471
BXD09	0.383	0.135
CAST	1.099	0.36
CCcont	1.022	0.025
DS01	0.883	0.154
DS02	0.745	0.521
DS04	0.748	0.386
DS0c	-0.019	0.401
GP01	0.72	1.139
GP02	0.311	1.098
GP0c	0.208	0.24
NOD	0.919	0.285
NZO	-0.088	0.608
PWK	0.494	0.128
H37Rv_KO_CtpC	1.553	0.454
H37Rv_KO_CtpD	1.287	0.874
H37Rv_KO_Rv1272	2.221	0.69
H37Rv_KO_SugABC	0.898	-0.034
H37Rv_KO_MbtN	0.687	-0.616
Trans05	1.378	-0.469
macrophage_unactivated	0.767	-0.117
IL1	0.039	-1.16
Rapamycin	0.264	-0.405
Tcell	0.525	-0.365
GMCSF	1.333	0.615
IFNab	0.768	-0.46
IFNg	0.083	-0.569
IFNg_GMCSF1	0.289	0.057
Rv1432_day32	0.85	0.428
Rv1565c_day32	2.139	-0.648
secA2_input	0.182	1.522
delta_Rv3594	0.34	-0.326
delta_Rv3717	0.145	-0.596
delta_Rv3811	0.427	-0.36
delta_Rv0954	-0.225	-1.79
PonA1	0.516	0.029
EccD1_KO	0.947	0.608
EspI_KO	1.178	0.034
PE35_KO	0.84	0.572
PPE68_KO	0.579	0.118
glycerol2	-1.302	-1.886
lignocerate	-0.961	-1.465
oleate	-1.032	-0.8
phosphatidylcholine	-0.819	-1.335
acetate	-1.248	-1.682
glucAc	-0.722	-1.271
Rv0950ko	0.555	0.208
Rv1096ko	-0.347	0.238
Rv3684ko	-0.354	-0.17
delta_otsA_trehalose	-1.531	0.157