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 Rv1781c/malQ:

update plot	correlation	link to info on gene
Rv2077c/-	(cc=0.588)	info on Rv2077c/-
Rv2742c/-	(cc=0.5286)	info on Rv2742c/-
Rv3065/mmr	(cc=0.5262)	info on Rv3065/mmr
Rv1923/lipD	(cc=0.5023)	info on Rv1923/lipD
Rv2079/-	(cc=0.4898)	info on Rv2079/-
Rv1045/-	(cc=0.4896)	info on Rv1045/-
Rv1263/amiB2	(cc=0.4836)	info on Rv1263/amiB2
Rv1774/-	(cc=0.4798)	info on Rv1774/-
Rv3508/PE_PGRS54	(cc=0.4761)	info on Rv3508/PE_PGRS54
Rv2022c/-	(cc=0.4731)	info on Rv2022c/-

Correlation of Rv1781c/malQ with Rv2079/-

Normalized LFCs for Rv1781c/malQ:
(description and provenance of datasets)

	Rv1781c/malQ	Rv2079/-
Fe_supp_jason_reseq	-0.549	-0.123
low_pH_jason_reseq	-0.54	-0.415
NO_jason_reseq	-0.105	0.777
B6_jason_reseq	-0.496	-0.132
MHCII_jason_reseq	0.452	0.096
Isoniazid02	-0.544	-0.599
Rifampicin4	0.468	0.081
Ethambutol3	-0.426	-0.769
Meropenem3	0.226	0.362
Vancomycin16	-0.398	-0.451
Rv2680_day32	0.656	0.061
H37Rv_KO_MarP	0.0	0.26
hypoxia_3wks	-0.283	0.439
hypoxia_6wks	-0.278	0.067
glycerol	-0.072	-0.168
cholesterol	-0.311	-0.653
AJ	0.094	0.062
Bibs02	0.146	0.436
Bibs02c	0.565	0.0
BL6	-0.066	-0.69
BL6a	0.093	-0.109
BXD01	-0.443	-0.643
BXD010	-0.096	-0.428
BXD011	-0.209	0.12
BXD03	-0.541	0.082
BXD04	-0.546	0.452
BXD05	-0.174	-0.433
BXD06	-0.589	-0.32
BXD07	0.042	-0.025
BXD08	-0.192	-0.137
BXD09	-0.446	-0.245
CAST	0.279	0.465
CCcont	-0.74	-0.445
DS01	-0.214	0.352
DS02	-0.271	0.239
DS04	0.513	-0.51
DS0c	-0.465	-0.181
GP01	0.99	0.456
GP02	1.591	1.729
GP0c	0.908	0.253
NOD	0.451	0.932
NZO	0.153	0.403
PWK	0.273	-0.071
H37Rv_KO_CtpC	0.177	0.488
H37Rv_KO_CtpD	0.714	0.373
H37Rv_KO_Rv1272	0.246	0.699
H37Rv_KO_SugABC	0.576	-0.009
H37Rv_KO_MbtN	0.174	0.985
Trans05	0.428	0.941
macrophage_unactivated	-0.237	-0.23
IL1	-0.35	-0.386
Rapamycin	-0.123	-0.709
Tcell	-0.779	0.059
GMCSF	-0.721	-0.143
IFNab	0.0	-0.514
IFNg	0.134	-0.144
IFNg_GMCSF1	-0.292	-0.471
Rv1432_day32	0.57	0.13
Rv1565c_day32	-0.011	0.395
secA2_input	0.249	0.142
delta_Rv3594	-0.24	0.292
delta_Rv3717	0.284	0.544
delta_Rv3811	0.138	0.021
delta_Rv0954	0.183	0.102
PonA1	-0.095	-0.254
EccD1_KO	-0.207	0.378
EspI_KO	0.282	0.068
PE35_KO	-0.715	0.169
PPE68_KO	-0.745	0.259
glycerol2	0.502	0.364
lignocerate	0.436	0.554
oleate	0.384	0.074
phosphatidylcholine	0.65	0.619
acetate	-0.057	0.086
glucAc	-0.241	0.124
Rv0950ko	-0.054	0.196
Rv1096ko	0.211	0.636
Rv3684ko	-0.262	0.498
delta_otsA_trehalose	-0.034	-1.323