Figure 2.

Variably expressed lncRNAs and novel intergenic transcripts. Heatmaps illustrating the 368 lncRNAs (left) and 297 novel transcripts (right) with variable expression as defined by standard deviation >0.25 across 66 cancer samples. Transcripts with differential expression in at least one of the 17 two-class SAM analyses (top) were clustered separately from those transcripts not significantly differentially expressed (bottom). Normalized read data were median centered, hierarchically clustered and plotted on a low (green) to high (red) heatmap. Samples are grouped by cancer type; the number in parentheses indicates the number of libraries for each cancer type. Red and pink is used for libraries made from adenocarcinomas of breast, lung, colon and prostate, as well as normal breast, lung and colon. Orange and yellow show squamous cell carcinomas of the head and neck, skin, lung and other carcinomas: papillary urothelial carcinoma and nasopharyngeal carcinoma. Green indicates sarcomas with known translocations: endometrial stromal sarcoma, Ewing's sarcoma, extraskeletal myxoid chondrosarcoma, synovial sarcoma and myxoid liposarcoma. Blue shows other sarcomas: gastrointestinal stromal tumor, leiomyosarcoma and dedifferentiated liposarcoma. Normal samples and cancer samples were combined for hierarchical clustering, but are displayed separately for clarity. Samples are ordered according to Table S1 in Additional file 1. Breast, breast invasive ductal carcinoma; colon, colon adenocarcinoma; DDLPS, dedifferentiated liposarcoma; EMC, extraskeletal myxoid chondrosarcoma; ESS, endometrial stromal sarcoma; EWS, Ewing's sarcoma; GIST, gastrointestinal stromal tumor; HN SCC, head and neck squamous cell carcinoma; LMS, leiomyosarcoma; Lung, lung adenocarcinoma; Lung SCC, lung squamous cell carcinoma; MLS, myxoid liposarcoma; NPC, nasopharyngeal carcinoma; prostate, prostate adenocarcinoma; PUC, papillary urothelial carcinoma; Skin SCC, skin squamous cell carcinoma; SS, synovial sarcoma.