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 Rv0501/galE2:

update plot	correlation	link to info on gene
Rv0502/-	(cc=0.7955)	info on Rv0502/-
Rv2004c/-	(cc=0.6697)	info on Rv2004c/-
Rv2185c/TB16.3	(cc=0.6446)	info on Rv2185c/TB16.3
Rv0924c/mntH	(cc=0.6281)	info on Rv0924c/mntH
Rv0642c/mmaA4	(cc=0.6216)	info on Rv0642c/mmaA4
Rv3166c/-	(cc=0.6028)	info on Rv3166c/-
Rv2134c/-	(cc=0.5949)	info on Rv2134c/-
Rv0989c/grcC2	(cc=0.5834)	info on Rv0989c/grcC2
Rv3050c/-	(cc=0.5712)	info on Rv3050c/-
Rv2184c/-	(cc=0.5601)	info on Rv2184c/-

Correlation of Rv0501/galE2 with Rv3166c/-

Normalized LFCs for Rv0501/galE2:
(description and provenance of datasets)

	Rv0501/galE2	Rv3166c/-
Fe_supp_jason_reseq	0.819	1.028
low_pH_jason_reseq	0.398	0.482
NO_jason_reseq	0.9	0.087
B6_jason_reseq	-0.603	-1.11
MHCII_jason_reseq	0.81	-0.193
Isoniazid02	-0.566	0.412
Rifampicin4	0.171	-0.073
Ethambutol3	-0.632	0.501
Meropenem3	0.232	0.214
Vancomycin16	-1.544	0.21
Rv2680_day32	0.396	0.781
H37Rv_KO_MarP	0.492	0.183
hypoxia_3wks	0.586	0.0
hypoxia_6wks	0.334	-0.336
glycerol	1.084	0.803
cholesterol	0.87	0.497
AJ	0.961	0.861
Bibs02	-0.725	-0.621
Bibs02c	0.706	1.303
BL6	0.671	1.769
BL6a	1.462	2.045
BXD01	1.68	1.207
BXD010	0.367	0.811
BXD011	0.832	1.128
BXD03	0.843	1.462
BXD04	0.896	1.549
BXD05	0.688	1.91
BXD06	1.106	1.378
BXD07	1.499	1.851
BXD08	0.999	1.11
BXD09	1.5	1.744
CAST	-0.609	-0.284
CCcont	1.284	1.322
DS01	0.934	0.219
DS02	0.088	0.277
DS04	0.749	0.28
DS0c	1.384	0.082
GP01	1.371	-0.079
GP02	1.485	1.205
GP0c	1.012	0.694
NOD	0.846	1.009
NZO	-0.231	-0.525
PWK	-0.352	-1.138
H37Rv_KO_CtpC	-0.214	1.129
H37Rv_KO_CtpD	1.254	2.225
H37Rv_KO_Rv1272	1.287	0.296
H37Rv_KO_SugABC	0.579	0.159
H37Rv_KO_MbtN	1.465	-0.22
Trans05	1.139	0.097
macrophage_unactivated	1.102	0.71
IL1	-0.896	0.86
Rapamycin	0.203	1.019
Tcell	0.661	0.248
GMCSF	0.174	0.158
IFNab	0.278	1.128
IFNg	0.107	0.115
IFNg_GMCSF1	0.248	1.439
Rv1432_day32	0.759	0.931
Rv1565c_day32	-0.618	0.035
secA2_input	-0.391	-0.233
delta_Rv3594	-0.349	0.537
delta_Rv3717	0.323	-0.866
delta_Rv3811	-0.379	-0.235
delta_Rv0954	-1.056	-0.544
PonA1	-1.075	-0.922
EccD1_KO	-0.585	0.533
EspI_KO	1.001	0.639
PE35_KO	-0.061	0.359
PPE68_KO	-0.24	0.266
glycerol2	0.205	-0.319
lignocerate	-0.18	0.222
oleate	-0.398	-0.323
phosphatidylcholine	-0.636	0.088
acetate	0.289	0.53
glucAc	-0.365	0.233
Rv0950ko	-1.004	-1.101
Rv1096ko	-1.496	-1.143
Rv3684ko	-1.091	-0.789
delta_otsA_trehalose	-0.199	-0.826