Sample Set Annotation Tool: Gene expression before HAART initiation predicts HIV-infected individuals at risk of poor CD4+ T cell recovery

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Analysis of peripheral blood mononuclear cells (PBMCs) taken from 24 HIV-infected male participants before the start of highly active antiretroviral therapy (HAART).

Results identify biomarkers for the identification of HIV-infected participants that progress to good versus poor CD4+ T cell recovery after 48 weeks of HAART.

Hypothesis

Experimental Design

This retrospective study evaluated PBMC gene expression in cells taken within 2 weeks before intitiation of HAART from 24 recently HIV-infected individuals to identify genes whose expression is predictive of CD4+ T cell recovery after 48 weeks of HAART.

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

24 Samples Loaded: 24

Species

Human (Homo sapiens)

Sample Source

PBMC

Disease

HIV

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

Please log in in order to upload files.

Samples Preview

Sample ID	Age	!Sample_title	sex	batch	cell count (baseline cd4+ t cell count, cells/ul)
GSM477695	31 years	poor_recovery	Male	1	463.00
GSM477696	36 years	poor_recovery	Male	1	449.00
GSM477697	39 years	good_recovery	Male	1	226.00
GSM477698	38 years	good_recovery	Male	1	310.50
GSM477699	52 years	poor_recovery	Male	1	388.00

Please log in in order to upload files.

File
sampleset4000005_sampleannotations_edited.csv

Samples Viewer / Editor

All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.

Sample ID	Age	!Sample Title	Sex	Batch	Cell count (baseline cd4+ t cell count, cells/ul)	Subsequent drug regimen	Race	Cell type	Change in cell count (change in cd4+ t cell count, cells/ml)	Final cell count (final week 48 cd4+ t cell count, cells/ul)
GSM477695	31 years	poor_recovery	Male	1	463.00	NNRTI	White	PBMC	128.50	591.50
GSM477696	36 years	poor_recovery	Male	1	449.00	NNRTI	White	PBMC	99.00	548.00
GSM477697	39 years	good_recovery	Male	1	226.00	NNRTI	American Indian	PBMC	245.00	471.00
GSM477698	38 years	good_recovery	Male	1	310.50	NNRTI	White	PBMC	352.50	663.00
GSM477699	52 years	poor_recovery	Male	1	388.00	NNRTI	White	PBMC	-68.00	320.00
GSM477700	42 years	poor_recovery	Male	1	413.67	NNRTI	White	PBMC	90.33	504.00
GSM477701	24 years	good_recovery	Male	1	232.00	NNRTI	African American	PBMC	756.00	988.00
GSM477702	38 years	good_recovery	Male	1	285.00	NNRTI	White	PBMC	279.00	564.00
GSM477703	28 years	good_recovery	Male	1	413.50	NNRTI	White	PBMC	362.50	776.00
GSM477704	33 years	poor_recovery	Male	1	282.67	NNRTI	Asian	PBMC	26.33	309.00
GSM477705	28 years	poor_recovery	Male	1	383.00	NNRTI	White	PBMC	51.00	434.00
GSM477706	19 years	good_recovery	Male	1	226.00	NNRTI	White	PBMC	328.00	471.00
GSM477707	29 years	poor_recovery	Male	2	404.57	PI	White	PBMC	47.43	452.00
GSM477708	50 years	poor_recovery	Male	2	425.33	PI	White	PBMC	45.47	470.80
GSM477709	58 years	poor_recovery	Male	2	454.33	PI	White	PBMC	184.33	638.67
GSM477710	50 years	poor_recovery	Male	2	414.33	PI	White	PBMC	124.67	539.00
GSM477711	33 years	good_recovery	Male	2	221.50	PI	White	PBMC	569.50	791.00
GSM477712	24 years	poor_recovery	Male	2	362.00	PI	American Indian	PBMC	114.00	476.00
GSM477713	39 years	good_recovery	Male	2	200.67	PI	White	PBMC	283.33	484.00
GSM477714	34 years	poor_recovery	Male	2	315.75	PI	African American	PBMC	118.25	434.00
GSM477715	40 years	good_recovery	Male	2	224.00	PI	Asian	PBMC	454.00	678.00
GSM477716	37 years	good_recovery	Male	2	210.00	PI	Asian	PBMC	292.00	502.00
GSM477717	54 years	good_recovery	Male	2	272.50	PI	White	PBMC	533.50	806.00
GSM477718	27 years	good_recovery	Male	2	398.00	PI	White	PBMC	680.00	1078.00

Group Sets View in Gene Expression Browser

Name
All Samples	Default	View
In order to make new Group Sets or change settings, please log in.

Module Analysis

Group Set
All Samples

SIDRA