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 Rv1960c/parD1:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv2278/-	(cc=0.5592)	info on Rv2278/-
Rv2071c/cobM	(cc=0.5581)	info on Rv2071c/cobM
Rv0201c/-	(cc=0.5285)	info on Rv0201c/-
Rv1673c/-	(cc=0.5223)	info on Rv1673c/-
Rv0959A/vapB9	(cc=0.5068)	info on Rv0959A/vapB9
Rv1962A/vapB35	(cc=0.4945)	info on Rv1962A/vapB35
Rv1872c/lldD2	(cc=0.4874)	info on Rv1872c/lldD2
Rv2842c/-	(cc=0.4853)	info on Rv2842c/-
Rv2464c/-	(cc=0.4815)	info on Rv2464c/-
Rv1076/lipU	(cc=0.4539)	info on Rv1076/lipU

Correlation of Rv1960c/parD1 with Rv2278/-

Normalized LFCs for Rv1960c/parD1:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv1960c/parD1	Rv2278/-
Fe_supp_jason_reseq	-2.898	-0.826
low_pH_jason_reseq	-1.964	0.805
NO_jason_reseq	0.496	-0.78
B6_jason_reseq	-3.787	-1.946
MHCII_jason_reseq	-1.898	-0.839
Isoniazid02	0.426	0.322
Rifampicin4	0.523	1.118
Ethambutol3	0.461	1.45
Meropenem3	0.351	0.079
Vancomycin16	0.512	0.358
Rv2680_day32	1.551	-0.034
H37Rv_KO_MarP	-1.411	-0.38
hypoxia_3wks	-0.343	0.981
hypoxia_6wks	-1.238	-0.04
glycerol	1.271	-0.499
cholesterol	-0.512	0.132
AJ	-0.086	1.676
Bibs02	0.113	-0.028
Bibs02c	-0.537	0.662
BL6	0.503	-0.196
BL6a	0.408	0.72
BXD01	1.018	0.682
BXD010	-0.012	0.599
BXD011	-0.134	0.34
BXD03	1.063	0.716
BXD04	-0.046	0.948
BXD05	-0.101	0.811
BXD06	-0.181	0.462
BXD07	0.741	0.774
BXD08	0.607	0.461
BXD09	0.18	0.221
CAST	0.122	0.909
CCcont	-0.142	-0.251
DS01	-1.648	-0.096
DS02	-1.761	-0.044
DS04	-1.609	0.122
DS0c	-1.259	0.434
GP01	0.683	1.114
GP02	0.0	1.244
GP0c	0.982	0.677
NOD	-0.041	0.373
NZO	-0.074	1.003
PWK	0.087	1.6
H37Rv_KO_CtpC	0.0	0.631
H37Rv_KO_CtpD	-0.514	0.0
H37Rv_KO_Rv1272	0.203	0.191
H37Rv_KO_SugABC	-1.324	-0.161
H37Rv_KO_MbtN	0.596	0.982
Trans05	-0.247	0.787
macrophage_unactivated	-2.553	-0.518
IL1	-2.142	-1.548
Rapamycin	-2.894	-1.602
Tcell	-1.496	-1.251
GMCSF	-2.102	-0.618
IFNab	-0.795	-1.521
IFNg	-1.31	-0.54
IFNg_GMCSF1	-2.963	-0.107
Rv1432_day32	0.164	1.314
Rv1565c_day32	0.0	-0.133
secA2_input	0.737	-0.409
delta_Rv3594	-1.21	-0.046
delta_Rv3717	-0.625	-0.229
delta_Rv3811	0.302	-0.348
delta_Rv0954	0.262	0.234
PonA1	0.211	-0.321
EccD1_KO	1.46	1.161
EspI_KO	0.99	1.397
PE35_KO	0.578	1.747
PPE68_KO	1.395	1.549
glycerol2	0.478	-0.185
lignocerate	-0.158	-0.329
oleate	0.77	0.044
phosphatidylcholine	0.374	-0.326
acetate	-0.387	0.781
glucAc	-0.659	1.395
Rv0950ko	-0.763	0.582
Rv1096ko	0.395	0.458
Rv3684ko	-2.266	-0.026
delta_otsA_trehalose	0.047	0.895