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Blood, Vol. 109, Issue 5, 2156-2164, March 1, 2007
Gene-expression profiling of systemic anaplastic large-cell lymphoma reveals differences based on ALK status and two distinct morphologic ALK+ subtypes
Blood Lamant et al.
109: 2156
Supplemental materials for: Lamant et al, Blood, Vol. 109, Issue 5, 2156-2164
Files in this Data Supplement:
- Table S1. Pattern discovery (XLS, 97 KB)
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The sheet “genes used in Figure 1A” lists the 495 probe sets (corresponding to the top 2.5% most varying expression profiles across the 32 ALCL samples) used in Figure 1A. The sheet “genes used in Figure 1B” lists the 198 probe sets (corresponding to the top 1% most varying expression profiles across the 25 ALK+ ALCL samples) used in Figure 1B. For each probe set, Entrez Gene (Entrez Gene identifier), symbol (HUGO gene symbol), and title (gene title) are given.
- Table S2. Pattern discovery of 25 ALK+ ALCL (XLS, 368 KB)
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This table is related to the list of the 841 probe sets (see sheet “t tests”) significantly differentially expressed between groups C1′ and C2′, which are defined in Figure 1B (pattern discovery of the 25 ALK+ ALCL tumor samples). Probe sets were selected using a t test with a P value threshold of 10–3 (probe sets for which both groups had a geometric mean intensity less than 100 were filtered). The list of selected probe sets is divided into 2 sublists: (i) probe sets up-regulated in the first group (C1′) compared with the second group (C2′) (ratio >1) and (ii) probe sets down-regulated in the first group compared with the second group (ratio <1). A GO (gene ontology) analysis is provided for the complete list and the 2 sublists of probe sets (see sheets “GO all genes, GO genes UP in group 1, GO genes DOWN in group 1”). Given a list of probe sets, a GO analysis measures the enrichment (using a hypergeometric test) of a GO term representation in this list relative to the entire chip (by mapping to distinct Entrez Gene identifiers). We selected GO terms corresponding to at least three genes (Entrez Gene identifiers) in the list of selected probe sets and yielding P values less than 10–3. Pathway analysis using the complete list of probe sets is also provided (see sheet “Pathways”).
Sheet “t tests” contains the following columns: Probe set, Symbol (HUGO gene symbol), Title (gene title), Entrez Gene (Entrez Gene identifier), Geom mean group1 (geometric mean intensity in the first group), Geom mean group2 (geometric mean intensity in the second group), Fold Change group1/group2 (ratio of geometric mean intensity in first group vs geometric mean intensity in second group), UP/DOWN in group1 (subsets of up-regulated and down-regulated probe sets in the first group compared with the second group).
Sheets “GO all genes, GO genes UP in group 1, and GO genes DOWN in group 1” contain the following columns:
• GO term: Gene Ontology term (description)
• GO id: Gene Ontology identifier
• No. related Entrez Gene in HG-U133A: number of (distinct) Entrez Gene identifiers related to the GO term in the whole chip
• No. related Entrez Gene in list: number of (distinct) Entrez Gene identifiers related to the GO term in the list of selected probe sets
• P value: P value of the hypergeometric test
• Entrez Gene: (distinct) Entrez Gene identifiers related to the GO term in the list of selected probe sets
• Symbol: (distinct) HUGO gene symbols related to the GO term in the list of selected probe sets
• Probe set: probe sets related to the GO term in the list of selected probe sets
• Ontology: Ontology category
Sheet “Pathways” contains the following columns:
• Genes overlapping with pathways: pathway name
• No. related genes in list: number of distinct HUGO gene symbols related to the pathway in the list of selected probe sets
• P value: P value of the Fisher test (see the Methods section)
• Group 1/group 2: UP indicates that HUGO gene symbols related to the pathway in the list of selected probe sets are globally up-regulated in group 1 compared with group 2. Down indicates that HUGO gene symbols related to the pathway in the list of selected probe sets are globally down-regulated in group 1 compared with group 2.
- Table S3. Molecular signature associated with ALK status (XLS, 104 KB)
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This table is related to the list of the 347 probe sets significantly differentially expressed between ALK+ ALCL and ALK– ALCL. These probe sets were selected using a t test with a P value threshold of 10–3. See Table S2 legend for sheets “t tests,” “GO all genes,” “GO genes UP in group 2,” “GO genes DOWN in group 2.”
- Table S4. Molecular signature associated with morphological features (XLS, 255 KB)
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This table is related to the list of the 491 probe sets significantly differentially expressed between common type ALCL and morphologic variants. These probe sets were selected using a t test with a P value threshold of 10–2. See Table S2 legend for sheets “t tests,” “GO all genes,” “GO genes UP in group 2,” “GO genes DOWN in group 2,” and “Pathways.”
- Table S5. Consensus cluster analysis (XLS, 34 KB)
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A consensus cluster analysis identified 5 consensus clusters A, B, C, D, and E (defined as samples that clustered together at least 95% of the time in the 24 dendograms). Common type ALCLs were primarily found in 4 consensus clusters—A (6/7), B (4/4), D (3/3), and E (2/3)—whereas morphologic variant ALCLs were primarily grouped in the consensus cluster C (7/9).
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