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 Rv1772/-:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv1964/yrbE3A	(cc=0.4517)	info on Rv1964/yrbE3A
Rv1892/-	(cc=0.4144)	info on Rv1892/-
Rv0057/-	(cc=0.4116)	info on Rv0057/-
Rv3618/-	(cc=0.4083)	info on Rv3618/-
Rv0364/-	(cc=0.4051)	info on Rv0364/-
Rv2789c/fadE21	(cc=0.4042)	info on Rv2789c/fadE21
Rv2480c/-	(cc=0.4005)	info on Rv2480c/-
Rv2495c/bkdC	(cc=0.4001)	info on Rv2495c/bkdC
Rv0222/echA1	(cc=0.3902)	info on Rv0222/echA1
Rv1720c/vapC12	(cc=0.3862)	info on Rv1720c/vapC12

Correlation of Rv1772/- with Rv1964/yrbE3A

Normalized LFCs for Rv1772/-:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv1772/-	Rv1964/yrbE3A
Fe_supp_jason_reseq	-3.334	-0.073
low_pH_jason_reseq	-1.822	-0.617
NO_jason_reseq	-0.68	-0.462
B6_jason_reseq	-2.688	-2.076
MHCII_jason_reseq	-3.659	-0.791
Isoniazid02	0.354	0.354
Rifampicin4	-1.543	0.761
Ethambutol3	1.497	0.846
Meropenem3	0.973	0.583
Vancomycin16	0.154	0.615
Rv2680_day32	-0.828	-1.004
H37Rv_KO_MarP	-0.799	-0.26
hypoxia_3wks	-1.049	0.283
hypoxia_6wks	-1.138	-0.044
glycerol	-1.546	-1.295
cholesterol	0.384	-0.733
AJ	0.65	0.254
Bibs02	0.107	-0.596
Bibs02c	0.082	0.045
BL6	1.146	0.527
BL6a	1.551	-0.221
BXD01	-0.501	-0.106
BXD010	-1.496	-0.215
BXD011	0.099	0.438
BXD03	0.851	0.712
BXD04	-0.668	0.135
BXD05	1.785	-0.197
BXD06	-0.967	0.097
BXD07	0.345	0.104
BXD08	-0.911	0.667
BXD09	-0.18	-0.095
CAST	-0.295	-0.966
CCcont	-0.49	0.193
DS01	-0.527	-0.662
DS02	2.083	-0.422
DS04	0.603	-0.436
DS0c	-1.752	-0.154
GP01	0.307	1.515
GP02	-1.275	-1.02
GP0c	-1.109	-0.057
NOD	3.695	0.758
NZO	-0.256	-0.692
PWK	1.421	-0.672
H37Rv_KO_CtpC	1.419	0.933
H37Rv_KO_CtpD	-1.405	1.268
H37Rv_KO_Rv1272	0.0	0.787
H37Rv_KO_SugABC	-1.22	-1.387
H37Rv_KO_MbtN	2.598	1.105
Trans05	-1.609	0.554
macrophage_unactivated	0.754	0.297
IL1	-0.086	-0.383
Rapamycin	1.093	-0.04
Tcell	1.844	0.163
GMCSF	-0.945	0.28
IFNab	0.088	0.475
IFNg	2.392	1.36
IFNg_GMCSF1	2.91	0.383
Rv1432_day32	-2.282	0.039
Rv1565c_day32	0.0	-0.272
secA2_input	-0.941	0.24
delta_Rv3594	1.225	0.405
delta_Rv3717	0.603	0.258
delta_Rv3811	-1.022	0.721
delta_Rv0954	-1.292	0.669
PonA1	-0.793	0.084
EccD1_KO	-2.131	-0.664
EspI_KO	-2.059	-0.662
PE35_KO	-1.619	-0.379
PPE68_KO	-0.921	-0.31
glycerol2	0.988	0.153
lignocerate	1.841	0.509
oleate	-1.494	-0.634
phosphatidylcholine	0.794	0.136
acetate	2.031	1.124
glucAc	0.157	0.876
Rv0950ko	0.582	0.151
Rv1096ko	-0.211	0.48
Rv3684ko	1.89	0.888
delta_otsA_trehalose	-1.296	0.359