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 Rv3711c/dnaQ:

update plot	correlation	link to info on gene
Rv0701/rplC	(cc=0.5726)	info on Rv0701/rplC
Rv3673c/-	(cc=0.5346)	info on Rv3673c/-
Rv0057/-	(cc=0.51)	info on Rv0057/-
Rv2882c/frr	(cc=0.4876)	info on Rv2882c/frr
Rv2678c/hemE	(cc=0.4809)	info on Rv2678c/hemE
Rv2622/-	(cc=0.4761)	info on Rv2622/-
Rv3763/lpqH	(cc=0.4662)	info on Rv3763/lpqH
Rv3670/ephE	(cc=0.4655)	info on Rv3670/ephE
Rv2164c/-	(cc=0.4651)	info on Rv2164c/-
Rv0648/-	(cc=0.4575)	info on Rv0648/-

Correlation of Rv3711c/dnaQ with Rv0648/-

Normalized LFCs for Rv3711c/dnaQ:
(description and provenance of datasets)

	Rv3711c/dnaQ	Rv0648/-
Fe_supp_jason_reseq	-0.433	-0.423
low_pH_jason_reseq	-0.047	-0.159
NO_jason_reseq	-0.074	-0.06
B6_jason_reseq	-0.604	0.75
MHCII_jason_reseq	-0.194	0.848
Isoniazid02	-0.167	0.311
Rifampicin4	-0.571	0.485
Ethambutol3	-0.209	0.174
Meropenem3	1.414	0.625
Vancomycin16	-0.332	-0.077
Rv2680_day32	0.627	0.089
H37Rv_KO_MarP	-0.238	0.251
hypoxia_3wks	-0.439	0.124
hypoxia_6wks	-0.328	0.127
glycerol	1.463	1.027
cholesterol	0.32	0.486
AJ	0.0	0.624
Bibs02	-0.086	0.148
Bibs02c	0.788	0.374
BL6	0.599	0.278
BL6a	0.375	-0.053
BXD01	-0.392	-0.387
BXD010	-0.092	-0.353
BXD011	0.157	-0.149
BXD03	0.175	-0.036
BXD04	-0.01	-0.124
BXD05	0.47	0.102
BXD06	0.209	-0.164
BXD07	0.042	-0.154
BXD08	0.06	0.055
BXD09	-0.089	-0.341
CAST	0.522	0.454
CCcont	-0.012	-0.201
DS01	0.89	0.756
DS02	0.44	0.548
DS04	0.645	1.15
DS0c	0.479	0.492
GP01	-0.173	0.365
GP02	0.068	0.819
GP0c	0.517	0.238
NOD	-0.124	0.5
NZO	0.377	0.426
PWK	0.696	0.253
H37Rv_KO_CtpC	-1.011	-0.331
H37Rv_KO_CtpD	0.811	0.762
H37Rv_KO_Rv1272	0.837	-0.371
H37Rv_KO_SugABC	0.921	0.753
H37Rv_KO_MbtN	-0.228	-0.022
Trans05	0.413	0.034
macrophage_unactivated	-0.893	-0.603
IL1	-0.412	0.314
Rapamycin	0.028	-0.193
Tcell	-0.424	-0.622
GMCSF	-0.217	0.211
IFNab	0.209	0.042
IFNg	0.251	-0.305
IFNg_GMCSF1	0.622	0.022
Rv1432_day32	0.175	-0.242
Rv1565c_day32	-0.499	0.27
secA2_input	1.19	0.969
delta_Rv3594	0.889	0.754
delta_Rv3717	1.055	0.673
delta_Rv3811	-0.034	0.344
delta_Rv0954	-0.234	0.098
PonA1	0.436	0.188
EccD1_KO	-1.25	0.437
EspI_KO	-0.91	-0.094
PE35_KO	-1.388	-0.324
PPE68_KO	-1.523	-0.47
glycerol2	0.345	0.154
lignocerate	0.487	0.639
oleate	-0.553	0.237
phosphatidylcholine	-0.129	0.282
acetate	0.387	0.387
glucAc	0.267	0.468
Rv0950ko	0.606	0.386
Rv1096ko	0.781	1.276
Rv3684ko	0.819	0.108
delta_otsA_trehalose	0.657	-0.912