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 Rv0066c/icd2:

update plot	correlation	link to info on gene
Rv3754/tyrA	(cc=0.6527)	info on Rv3754/tyrA
Rv0211/pckA	(cc=0.584)	info on Rv0211/pckA
Rv1610/-	(cc=0.5691)	info on Rv1610/-
Rv2524c/fas	(cc=0.569)	info on Rv2524c/fas
Rv1543/-	(cc=0.551)	info on Rv1543/-
Rv1457c/-	(cc=0.5495)	info on Rv1457c/-
Rv2202c/adoK	(cc=0.5306)	info on Rv2202c/adoK
Rv1120c/-	(cc=0.5241)	info on Rv1120c/-
Rv1872c/lldD2	(cc=0.5169)	info on Rv1872c/lldD2
Rv3410c/guaB3	(cc=0.5025)	info on Rv3410c/guaB3

Correlation of Rv0066c/icd2 with Rv1872c/lldD2

Normalized LFCs for Rv0066c/icd2:
(description and provenance of datasets)

	Rv0066c/icd2	Rv1872c/lldD2
Fe_supp_jason_reseq	0.415	0.493
low_pH_jason_reseq	0.0	-0.893
NO_jason_reseq	0.0	-0.971
B6_jason_reseq	0.0	-1.228
MHCII_jason_reseq	0.0	-1.417
Isoniazid02	1.752	0.418
Rifampicin4	0.325	-0.114
Ethambutol3	2.251	0.854
Meropenem3	2.259	0.158
Vancomycin16	0.162	0.48
Rv2680_day32	0.0	-0.449
H37Rv_KO_MarP	0.957	-0.591
hypoxia_3wks	0.0	1.12
hypoxia_6wks	-0.288	1.533
glycerol	0.0	1.369
cholesterol	0.0	0.764
AJ	0.0	0.062
Bibs02	0.0	-0.285
Bibs02c	0.0	-0.634
BL6	0.0	0.128
BL6a	0.198	-0.296
BXD01	0.0	0.164
BXD010	0.0	0.54
BXD011	0.782	0.304
BXD03	0.0	0.252
BXD04	0.0	0.208
BXD05	0.256	1.003
BXD06	0.0	0.469
BXD07	0.0	0.575
BXD08	0.0	0.478
BXD09	0.0	0.318
CAST	0.0	-1.313
CCcont	0.525	0.04
DS01	0.0	-1.098
DS02	0.0	0.871
DS04	0.194	0.0
DS0c	0.0	-0.22
GP01	0.0	-0.021
GP02	0.0	-0.764
GP0c	0.13	0.442
NOD	0.0	-0.35
NZO	0.0	-0.273
PWK	0.0	-0.355
H37Rv_KO_CtpC	0.162	1.363
H37Rv_KO_CtpD	0.127	0.774
H37Rv_KO_Rv1272	0.0	1.259
H37Rv_KO_SugABC	0.42	1.162
H37Rv_KO_MbtN	1.147	0.564
Trans05	0.0	0.414
macrophage_unactivated	-1.411	-1.515
IL1	-1.326	-2.928
Rapamycin	-1.372	-2.056
Tcell	-0.671	-5.002
GMCSF	-1.545	-1.935
IFNab	0.0	2.174
IFNg	-1.563	-6.0
IFNg_GMCSF1	-1.838	-5.247
Rv1432_day32	0.0	-0.468
Rv1565c_day32	0.0	-0.224
secA2_input	2.453	1.312
delta_Rv3594	0.0	-0.153
delta_Rv3717	1.067	-0.389
delta_Rv3811	0.0	-0.225
delta_Rv0954	0.627	-0.6
PonA1	0.0	-0.697
EccD1_KO	-0.635	1.141
EspI_KO	-0.265	0.388
PE35_KO	-0.271	0.747
PPE68_KO	0.278	0.326
glycerol2	0.193	0.301
lignocerate	0.0	-0.276
oleate	0.0	0.899
phosphatidylcholine	0.0	0.342
acetate	0.229	-1.189
glucAc	0.0	-0.983
Rv0950ko	-1.294	-0.051
Rv1096ko	-1.641	-0.772
Rv3684ko	-1.985	-0.891
delta_otsA_trehalose	0.468	1.781