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 Rv1468c/PE_PGRS29:

update plot	correlation	link to info on gene
Rv2205c/-	(cc=0.5487)	info on Rv2205c/-
Rv3344c/PE_PGRS49	(cc=0.4809)	info on Rv3344c/PE_PGRS49
Rv1840c/PE_PGRS34	(cc=0.4791)	info on Rv1840c/PE_PGRS34
Rv3892c/PPE69	(cc=0.4789)	info on Rv3892c/PPE69
Rv1004c/-	(cc=0.4679)	info on Rv1004c/-
Rv1452c/PE_PGRS28	(cc=0.463)	info on Rv1452c/PE_PGRS28
Rv1992c/ctpG	(cc=0.4583)	info on Rv1992c/ctpG
Rv0250c/-	(cc=0.4558)	info on Rv0250c/-
Rv0492c/-	(cc=0.4489)	info on Rv0492c/-
Rv2519/PE26	(cc=0.4469)	info on Rv2519/PE26

Correlation of Rv1468c/PE_PGRS29 with Rv3344c/PE_PGRS49

Normalized LFCs for Rv1468c/PE_PGRS29:
(description and provenance of datasets)

	Rv1468c/PE_PGRS29	Rv3344c/PE_PGRS49
Fe_supp_jason_reseq	0.425	-1.058
low_pH_jason_reseq	0.274	-1.604
NO_jason_reseq	-1.229	-0.845
B6_jason_reseq	-0.718	-0.895
MHCII_jason_reseq	-0.801	-0.171
Isoniazid02	0.303	1.292
Rifampicin4	1.968	0.948
Ethambutol3	1.278	2.134
Meropenem3	1.473	4.472
Vancomycin16	0.43	0.276
Rv2680_day32	-0.64	-0.261
H37Rv_KO_MarP	-0.049	0.505
hypoxia_3wks	-0.694	-0.933
hypoxia_6wks	-0.735	-1.357
glycerol	0.0	2.652
cholesterol	-0.388	1.799
AJ	1.612	1.861
Bibs02	0.389	0.823
Bibs02c	0.0	2.53
BL6	-0.835	-0.53
BL6a	0.0	1.121
BXD01	0.235	0.89
BXD010	-0.675	-1.192
BXD011	-0.078	-0.762
BXD03	-0.2	0.459
BXD04	0.024	0.156
BXD05	0.308	-0.235
BXD06	-0.428	-0.621
BXD07	0.339	0.388
BXD08	0.519	-0.111
BXD09	0.054	-0.386
CAST	0.415	0.179
CCcont	0.168	-0.462
DS01	0.652	-0.488
DS02	0.789	0.113
DS04	1.835	1.127
DS0c	-0.178	-0.52
GP01	1.93	0.754
GP02	0.863	0.963
GP0c	1.155	-0.841
NOD	-0.436	-0.322
NZO	0.751	0.344
PWK	0.254	-0.163
H37Rv_KO_CtpC	1.094	0.205
H37Rv_KO_CtpD	2.032	1.136
H37Rv_KO_Rv1272	1.204	2.135
H37Rv_KO_SugABC	0.346	0.101
H37Rv_KO_MbtN	1.692	1.843
Trans05	-0.193	0.964
macrophage_unactivated	-0.117	-0.9
IL1	-0.169	-2.856
Rapamycin	-0.608	-3.182
Tcell	0.059	-3.138
GMCSF	0.143	-1.127
IFNab	-0.599	-3.622
IFNg	-1.141	-2.771
IFNg_GMCSF1	0.798	-1.668
Rv1432_day32	0.07	1.031
Rv1565c_day32	-1.33	-1.579
secA2_input	-0.462	0.02
delta_Rv3594	0.6	4.285
delta_Rv3717	0.865	2.782
delta_Rv3811	0.708	2.231
delta_Rv0954	1.499	1.371
PonA1	0.99	2.185
EccD1_KO	-0.523	0.132
EspI_KO	-0.787	0.302
PE35_KO	-0.505	0.117
PPE68_KO	-0.291	0.064
glycerol2	-0.22	1.078
lignocerate	0.033	1.432
oleate	0.057	0.951
phosphatidylcholine	-0.262	1.032
acetate	-0.163	0.086
glucAc	-0.491	1.829
Rv0950ko	0.202	0.76
Rv1096ko	-0.127	0.956
Rv3684ko	0.177	1.965
delta_otsA_trehalose	0.284	0.654