Sample Set Annotation Tool: Expression data for derivation of septic shock subgroups

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Background: Septic shock is a heterogeneous syndrome within which probably exist several biological subclasses. Discovery and identification of septic shock subclasses could provide the foundation for the design of more specifically targeted therapies. Herein we tested the hypothesis that pediatric septic shock subclasses can be discovered through genome-wide expression profiling. Methods: Genome-wide expression profiling was conducted using whole blood-derived RNA from 98 children with septic shock, followed by a series of bioinformatic approaches targeted at subclass discovery and characterization. Results: Three putative subclasses (subclasses A, B, and C) were initially identified based on an empiric, discovery-oriented expression filter and unsupervised hierarchical clustering. Statistical comparison of the 3 putative subclasses (ANOVA, Bonferonni correction, p < 0.05) identified 6,934 differentially regulated genes. K means clustering of these 6,934 genes generated 10 coordinately regulated gene clusters corresponding to multiple signaling and metabolic pathways, all of which were differentially regulated across the 3 subclasses. Leave one out cross validation procedures indentified 100 genes having the strongest predictive values for subclass identification. Forty-four of these 100 genes corresponded to signaling pathways relevant to the adaptive immune system and glucocorticoid receptor signaling, the majority of which were repressed in subclass A patients. Subclass A patients were also characterized by repression of genes corresponding to zinc-related biology. Phenotypic analyses revealed that subclass A patients were younger, had a higher illness severity, and a higher mortality rate than patients in subclasses B and C. Conclusions: Genome-wide expression profiling can identify pediatric septic shock subclasses having clinically relevant phenotypes.

Hypothesis

Experimental Design

Expression data from 98 children with septic shock and 32 normal controls were generated using whole blood-derived RNA samples representing the first 24 hours of admission to the pediatric intensive care unit. The controls were used for normalization. Subsequently, we used the expression data to derive expression-based subclasses of patients using discovery oriented expression and statistical filters, followed by unsupervised hierarchical clustering.

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

130 Samples Loaded: 130

Species

Human (Homo sapiens)

Sample Source

Whole Blood , Neonatal , Pediatric

Disease

Sepsis

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample Title	tissue	group	Age (years)	Disease state
GSM648590	Septic Shock_biological rep1 01-0013	whole blood	A	9.4	septic shock patient
GSM648591	Septic Shock_biological rep2 01-0014	whole blood	C	3	septic shock patient
GSM648592	Septic Shock_biological rep3 01-0019	whole blood	C	2.1	septic shock patient
GSM648593	Septic Shock_biological rep4 01-0021	whole blood	B	1.9	septic shock patient
GSM648594	Septic Shock_biological rep5 01-0024	whole blood	B	0.8	septic shock patient

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File

GSE26440 modified.csv Sample Set Spreadsheet

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Sample ID	!Sample Title	Tissue	Group	Age (years)	Disease state	Group 1	Group 2	Outcome	Group name
GSM648590	Septic Shock_biological rep1 01-0013	whole blood	A	9.4	septic shock patient	children	children-septic shock patient	Nonsurvivor	children 3 yrs and older
GSM648591	Septic Shock_biological rep2 01-0014	whole blood	C	3	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648592	Septic Shock_biological rep3 01-0019	whole blood	C	2.1	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648593	Septic Shock_biological rep4 01-0021	whole blood	B	1.9	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648594	Septic Shock_biological rep5 01-0024	whole blood	B	0.8	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648595	Septic Shock_biological rep6 01-0025	whole blood	A	0.3	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648596	Septic Shock_biological rep7 01-0026	whole blood	A	9.1	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648597	Septic Shock_biological rep8 01-0030	whole blood	C	0.6	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648598	Septic Shock_biological rep9 01-0033A	whole blood	B	2.6	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648599	Septic Shock_biological rep10 01-0045A	whole blood	B	8.8	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648600	Septic Shock_biological rep11 01-0049A	whole blood	B	0.9	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648601	Septic Shock_biological rep12 01-0051A	whole blood	B	4.5	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648602	Septic Shock_biological rep13 01-0052A	whole blood	B	2	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648603	Septic Shock_biological rep14 01-0053A	whole blood	C	0.5	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648604	Septic Shock_biological rep15 01-0064	whole blood	B	2.4	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648605	Septic Shock_biological rep16 01-0068	whole blood	A	0.1	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648606	Septic Shock_biological rep17 01-0069	whole blood	C	0.8	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648607	Septic Shock_biological rep18 01-0071	whole blood	C	2.7	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648608	Septic Shock_biological rep19 01-0072	whole blood	B	6.8	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648609	Septic Shock_biological rep20 01-0073	whole blood	B	7.1	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648610	Septic Shock_biological rep21 01-0074	whole blood	B	7.3	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648611	Septic Shock_biological rep22 01-0077	whole blood	C	4.4	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648612	Septic Shock_biological rep23 01-0078	whole blood	C	2.8	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648613	Septic Shock_biological rep24 01-0079	whole blood	C	0.3	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648614	Septic Shock_biological rep25 01-0080	whole blood	B	3	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648615	Septic Shock_biological rep26 01-0007A	whole blood	A	3.7	septic shock patient	children	children-septic shock patient	Nonsurvivor	children 3 yrs and older
GSM648616	Septic Shock_biological rep27 01-0034A	whole blood	C	2.7	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648617	Septic Shock_biological rep28 01-0036A	whole blood	C	2.7	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648618	Septic Shock_biological rep29 01-0044A	whole blood	A	0.1	septic shock patient	infant	infant-septic shock patient	Nonsurvivor	infant
GSM648619	Septic Shock_biological rep30 01-0047	whole blood	C	0.7	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648620	Septic Shock_biological rep31 01-0058A	whole blood	A	0	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648621	Septic Shock_biological rep32 01-0059A	whole blood	B	1.6	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648622	Septic Shock_biological rep33 01-0060A	whole blood	B	1.1	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648623	Septic Shock_biological rep34 01-0061A	whole blood	B	1.9	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648624	Septic Shock_biological rep35 01-0062A	whole blood	B	2.2	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648625	Septic Shock_biological rep36 05-0007	whole blood	B	4.2	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648626	Septic Shock_biological rep37 01-0066A	whole blood	C	2.3	septic shock patient	toddler	toddler-septic shock patient	Nonsurvivor	toddler
GSM648627	Septic Shock_biological rep38 01-0070	whole blood	C	7.2	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648628	Septic Shock_biological rep39 01-0086	whole blood	C	0	septic shock patient	infant	infant-septic shock patient	Nonsurvivor	infant
GSM648629	Septic Shock_biological rep40 01-0088	whole blood	B	2.8	septic shock patient	toddler	toddler-septic shock patient	Nonsurvivor	toddler
GSM648630	Control_biological rep1 01-0104	whole blood	n/a	3.3	normal control	children	children-normal control	n/a	children control
GSM648631	Control_biological rep2 01-0105	whole blood	n/a	0.9	normal control	infant	infant-normal control	n/a	infant control
GSM648632	Control_biological rep3 01-0106	whole blood	n/a	5.3	normal control	children	children-normal control	n/a	children control
GSM648633	Septic Shock_biological rep41 02-0001	whole blood	B	7.3	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648634	Septic Shock_biological rep42 02-0002A	whole blood	B	5.7	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648635	Septic Shock_biological rep43 04-0003	whole blood	A	0.9	septic shock patient	infant	infant-septic shock patient	Nonsurvivor	infant
GSM648636	Septic Shock_biological rep44 04-0005	whole blood	B	1.6	septic shock patient	toddler	toddler-septic shock patient	Nonsurvivor	toddler
GSM648637	Control_biological rep4 04-0010C	whole blood	n/a	0	normal control	infant	infant-normal control	n/a	infant control
GSM648638	Control_biological rep5 04-0010	whole blood	n/a	0	normal control	infant	infant-normal control	Survivor	infant control
GSM648639	Control_biological rep6 04-0011C	whole blood	n/a	2.9	normal control	toddler	toddler-normal control	n/a	toddler control
GSM648640	Control_biological rep7 04-0011	whole blood	n/a	2.9	normal control	toddler	toddler-normal control	Survivor	toddler control
GSM648641	Control_biological rep8 04-0015	whole blood	n/a	0	normal control	infant	infant-normal control	n/a	infant control
GSM648642	Septic Shock_biological rep45 05-0003	whole blood	A	7.3	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648643	Septic Shock_biological rep46 05-0006	whole blood	A	2.3	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648644	Septic Shock_biological rep47 05-0008	whole blood	B	9	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648645	Septic Shock_biological rep48 05-0010	whole blood	A	0.2	septic shock patient	infant	infant-septic shock patient	Nonsurvivor	infant
GSM648646	Septic Shock_biological rep49 05-0011	whole blood	A	0	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648647	Septic Shock_biological rep50 06-0001	whole blood	A	0.3	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648648	Septic Shock_biological rep51 06-0003	whole blood	B	2.5	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648649	Septic Shock_biological rep52 06-0004	whole blood	A	0	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648650	Septic Shock_biological rep53 06-0006	whole blood	A	2.2	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648651	Septic Shock_biological rep54 06-0009A	whole blood	B	5.1	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648652	Septic Shock_biological rep55 07-0002	whole blood	B	10.9	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648653	Septic Shock_biological rep56 07-0006A	whole blood	B	6	septic shock patient	children	children-septic shock patient	Nonsurvivor	children 3 yrs and older
GSM648654	Septic Shock_biological rep57 07-0004	whole blood	C	0.7	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648655	Septic Shock_biological rep58 09-0001	whole blood	B	1.9	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648656	Septic Shock_biological rep59 09-0002	whole blood	A	2.3	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648657	Septic Shock_biological rep60 10-0001	whole blood	B	5.3	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648658	Septic Shock_biological rep61 10-0012	whole blood	B	10.8	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648659	Septic Shock_biological rep62 10-0017	whole blood	B	7.5	septic shock patient	children	children-septic shock patient	Nonsurvivor	children 3 yrs and older
GSM648660	Septic Shock_biological rep63 10-0020	whole blood	B	2.9	septic shock patient	toddler	toddler-septic shock patient	Nonsurvivor	toddler
GSM648661	Septic Shock_biological rep64 10-0003	whole blood	B	1.4	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648662	Septic Shock_biological rep65 10-0005	whole blood	B	7.8	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648663	Septic Shock_biological rep66 10-0009	whole blood	C	1.9	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648664	Septic Shock_biological rep67 10-0018	whole blood	B	1.5	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648665	Septic Shock_biological rep68 10-0019	whole blood	B	6.1	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648666	Septic Shock_biological rep69 10-0021A	whole blood	B	8.9	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648667	Septic Shock_biological rep70 11-0001	whole blood	A	1.8	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648668	Control_biological rep9 11-0008	whole blood	n/a	3.7	normal control	children	children-normal control	Survivor	children control
GSM648669	Control_biological rep10 11-0009	whole blood	n/a	0.7	normal control	infant	infant-normal control	Survivor	infant control
GSM648670	Septic Shock_biological rep71 11-0010	whole blood	C	1.4	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648671	Control_biological rep11 11-0011	whole blood	n/a	0.9	normal control	infant	infant-normal control	Survivor	infant control
GSM648672	Control_biological rep12 11-0012	whole blood	n/a	0	normal control	infant	infant-normal control	Survivor	infant control
GSM648673	Control_biological rep13 11-0013	whole blood	n/a	6.8	normal control	children	children-normal control	Survivor	children control
GSM648674	Control_biological rep14 11-0014	whole blood	n/a	0	normal control	infant	infant-normal control	Survivor	infant control
GSM648675	Septic Shock_biological rep72 11-0017	whole blood	A	0	septic shock patient	infant	infant-septic shock patient	Nonsurvivor	infant
GSM648676	Control_biological rep15 11-0018	whole blood	n/a	5.9	normal control	children	children-normal control	Survivor	children control
GSM648677	Control_biological rep16 11-0019	whole blood	n/a	9.7	normal control	children	children-normal control	Survivor	children control
GSM648678	Control_biological rep17 11-0020	whole blood	n/a	0.2	normal control	infant	infant-normal control	Survivor	infant control
GSM648679	Control_biological rep18 11-0027	whole blood	n/a	0.3	normal control	infant	infant-normal control	Survivor	infant control
GSM648680	Septic Shock_biological rep73 11-0029	whole blood	B	6.3	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648681	Control_biological rep19 11-0037	whole blood	n/a	0.3	normal control	infant	infant-normal control	Survivor	infant control
GSM648682	Septic Shock_biological rep74 11-0054A	whole blood	A	0.1	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648683	Septic Shock_biological rep75 11-0002	whole blood	B	1.3	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648684	Septic Shock_biological rep76 11-0007	whole blood	B	8	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648685	Septic Shock_biological rep77 11-0035	whole blood	B	1.7	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648686	Control_biological rep20 11-0036	whole blood	n/a	0.2	normal control	infant	infant-normal control	n/a	infant control
GSM648687	Control_biological rep21 11-0052C	whole blood	n/a	6	normal control	children	children-normal control	n/a	children control
GSM648688	Control_biological rep22 11-0052	whole blood	n/a	6	normal control	children	children-normal control	Survivor	children control
GSM648689	Control_biological rep23 11-0077	whole blood	n/a	1.9	normal control	toddler	toddler-normal control	n/a	toddler control
GSM648690	Control_biological rep24 11-0078	whole blood	n/a	0.7	normal control	infant	infant-normal control	n/a	infant control
GSM648691	Control_biological rep25 11-0080	whole blood	n/a	1.5	normal control	toddler	toddler-normal control	n/a	toddler control
GSM648692	Control_biological rep26 11-0081	whole blood	n/a	3	normal control	children	children-normal control	n/a	children control
GSM648693	Control_biological rep27 11-0082	whole blood	n/a	1.2	normal control	toddler	toddler-normal control	n/a	toddler control
GSM648694	Control_biological rep28 11-0083	whole blood	n/a	5.1	normal control	children	children-normal control	n/a	children control
GSM648695	Septic Shock_biological rep78 12-0002A	whole blood	A	1.4	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648696	Septic Shock_biological rep79 13-0002A	whole blood	A	7	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648697	Septic Shock_biological rep80 14-0002A	whole blood	B	5.9	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648698	Septic Shock_biological rep81 14-0004A	whole blood	A	0.1	septic shock patient	infant	infant-septic shock patient	Nonsurvivor	infant
GSM648699	Control_biological rep29 15-0001	whole blood	n/a	2	normal control	toddler	toddler-normal control	Survivor	toddler control
GSM648700	Control_biological rep30 15-0002	whole blood	n/a	1.8	normal control	toddler	toddler-normal control	Survivor	toddler control
GSM648701	Control_biological rep31 15-0003	whole blood	n/a	3.8	normal control	children	children-normal control	Survivor	children control
GSM648702	Septic Shock_biological rep82 15-0004	whole blood	B	1	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648703	Control_biological rep32 15-0005	whole blood	n/a	0	normal control	infant	infant-normal control	Survivor	infant control
GSM648704	Septic Shock_biological rep83 15-0007	whole blood	A	0.3	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648705	Septic Shock_biological rep84 15-0008	whole blood	A	9.4	septic shock patient	children	children-septic shock patient	Nonsurvivor	children 3 yrs and older
GSM648706	Septic Shock_biological rep85 15-0017	whole blood	A	0.3	septic shock patient	infant	infant-septic shock patient	Survivor	infant
GSM648707	Septic Shock_biological rep86 15-0011A	whole blood	C	1.5	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648708	Septic Shock_biological rep87 15-0012A	whole blood	A	0	septic shock patient	infant	infant-septic shock patient	Nonsurvivor	infant
GSM648709	Septic Shock_biological rep88 17-0001A	whole blood	B	8.2	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648710	Septic Shock_biological rep89 18-0002	whole blood	B	4.3	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older
GSM648711	Septic Shock_biological rep90 19-0001	whole blood	C	2	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648712	Septic Shock_biological rep91 19-0005	whole blood	C	2	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648713	Septic Shock_biological rep92 20-0002	whole blood	C	2	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648714	Septic Shock_biological rep93 20-0003	whole blood	C	2	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648715	Septic Shock_biological rep94 04-0004	whole blood	A	2.4	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648716	Septic Shock_biological rep95 21-0001	whole blood	C	2	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648717	Septic Shock_biological rep96 21-0003	whole blood	C	2	septic shock patient	toddler	toddler-septic shock patient	Survivor	toddler
GSM648718	Septic Shock_biological rep97 26-260611	whole blood	A	7.4	septic shock patient	children	children-septic shock patient	Nonsurvivor	children 3 yrs and older
GSM648719	Septic Shock_biological rep98 25-070603	whole blood	B	10	septic shock patient	children	children-septic shock patient	Survivor	children 3 yrs and older

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