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 Rv2896c/-:

update plot	correlation	link to info on gene
Rv1961/-	(cc=0.4625)	info on Rv1961/-
Rv0976c/-	(cc=0.4607)	info on Rv0976c/-
Rv2159c/-	(cc=0.4461)	info on Rv2159c/-
Rv3292/-	(cc=0.446)	info on Rv3292/-
Rv2012/-	(cc=0.426)	info on Rv2012/-
Rv0897c/-	(cc=0.4057)	info on Rv0897c/-
Rv0992c/-	(cc=0.404)	info on Rv0992c/-
Rv0994/moeA1	(cc=0.4033)	info on Rv0994/moeA1
Rv1452c/PE_PGRS28	(cc=0.3929)	info on Rv1452c/PE_PGRS28
Rv0222/echA1	(cc=0.3881)	info on Rv0222/echA1

Correlation of Rv2896c/- with Rv3292/-

Normalized LFCs for Rv2896c/-:
(description and provenance of datasets)

	Rv2896c/-	Rv3292/-
Fe_supp_jason_reseq	-0.685	-0.412
low_pH_jason_reseq	-0.932	-0.343
NO_jason_reseq	0.263	0.213
B6_jason_reseq	-0.482	0.563
MHCII_jason_reseq	-0.754	-0.023
Isoniazid02	0.764	0.872
Rifampicin4	-0.181	0.23
Ethambutol3	0.188	0.409
Meropenem3	0.114	0.229
Vancomycin16	0.058	0.608
Rv2680_day32	-0.456	0.055
H37Rv_KO_MarP	-0.051	0.861
hypoxia_3wks	-0.287	-0.534
hypoxia_6wks	-0.624	-0.522
glycerol	1.546	0.913
cholesterol	0.503	0.668
AJ	-0.128	0.035
Bibs02	0.654	-0.087
Bibs02c	-0.115	0.529
BL6	0.637	1.039
BL6a	0.103	0.191
BXD01	-0.299	0.153
BXD010	-0.223	-0.04
BXD011	-0.269	-0.146
BXD03	-0.562	0.24
BXD04	0.256	-0.174
BXD05	0.261	0.357
BXD06	-0.173	0.129
BXD07	0.082	0.237
BXD08	0.117	-0.052
BXD09	-0.182	-0.055
CAST	-0.108	-0.47
CCcont	-0.035	0.369
DS01	0.674	-0.055
DS02	0.767	0.285
DS04	0.706	0.408
DS0c	0.607	0.536
GP01	0.022	0.926
GP02	0.98	0.467
GP0c	0.465	0.289
NOD	0.792	0.216
NZO	-0.078	-0.754
PWK	-0.413	0.03
H37Rv_KO_CtpC	0.386	-0.427
H37Rv_KO_CtpD	0.78	0.652
H37Rv_KO_Rv1272	-0.435	-0.699
H37Rv_KO_SugABC	-1.474	-0.665
H37Rv_KO_MbtN	0.529	-0.164
Trans05	-0.377	0.18
macrophage_unactivated	0.18	0.0
IL1	0.516	1.02
Rapamycin	0.206	0.181
Tcell	-0.329	-0.039
GMCSF	-0.351	0.127
IFNab	-0.121	0.677
IFNg	0.489	0.219
IFNg_GMCSF1	0.179	0.364
Rv1432_day32	0.738	-0.308
Rv1565c_day32	0.491	-0.752
secA2_input	0.435	-0.454
delta_Rv3594	-0.286	-1.069
delta_Rv3717	0.083	-0.137
delta_Rv3811	0.0	-0.193
delta_Rv0954	-0.261	-0.491
PonA1	-0.485	-0.957
EccD1_KO	-0.145	0.411
EspI_KO	-0.083	0.439
PE35_KO	0.545	0.155
PPE68_KO	0.518	-0.106
glycerol2	-0.303	0.465
lignocerate	0.558	1.041
oleate	-0.072	-0.118
phosphatidylcholine	0.31	0.518
acetate	0.472	1.17
glucAc	0.304	0.728
Rv0950ko	0.172	0.274
Rv1096ko	0.829	1.128
Rv3684ko	0.576	1.585
delta_otsA_trehalose	-0.416	0.885