This document discusses various topics related to transcriptomics and lexico-syntactic analysis including: - The challenges of resolving gene names and identifiers from multiple databases. - Using text mining of biomedical abstracts to identify regulatory relationships between genes/proteins by parsing sentences and identifying relationships. - Integrating gene expression data from multiple experiments and species to infer functional links between genes based on correlations in expression profiles. - Other related resources discussed include the STRING database for predicting protein-protein interactions and the use of gene synonyms to integrate different types of biological data.

1. Transcriptomics and Lexico-syntactic Analysis (Yet another meaning of the TLA homonym) Lars Juhl Jensen EMBL Heidelberg

5. Number of uniquely resolvable names for each species 40,038 18,702 7.7 48,291 6,210 S. cerevisiae 15,865 116,712 6.6 132,577 20,006 M. musculus 18,944 181,186 7.1 200,130 27,936 H. sapiens 14,072 77,757 22,707 6.1 103,208 16,871 D. melanogaster 18,214 65,749 45,835 5.4 110,602 20,348 C. elegans 20,158 118,818 5.3 138,976 25,957 A. thaliana Uni-Gene SWALL Species specific Ratio Names Proteins

11. TIGERSearch is used for searching and browsing the large processed text corpus

12. Pattern recognize sentences in both active and passive voice

20. Non-linear normalization of intensities and correction for spatial effects Downloaded SMD data After intensity normalization Spatial bias estimate After spatial normalization

25. Proteins linked to the human mitotic checkpoint protein BUB1 Comments Description Identifier Cyclin-dependent kinases regulatory subunit CKS1_HUMAN Involved in cell cycle arrest Serine/threonine-protein kinase Chk1 CHK1_HUMAN Involved in mitotic regulation Serine/threonine-protein kinase NEK2 NEK2_HUMAN Cell cycle-dependent expression CRM1 protein O14980 May act as a negative regulator of entry into mitosis Wee1-like protein kinase WEE1_HUMAN Kinesin-like protein 2 KNS2_HUMAN Kinesin-like protein 2 Q96SE4 Kinesin-like protein KIF14 KF14_HUMAN HCAP-H protein Q15003 Contains six WD40 repeats L2DTL protein Q9NZJ0 Cyclin A2 CGA2_HUMAN Contains a PRY and a SPRY domain Hypothetical protein Q8N324 Polymyositis/scleroderma autoantigen 1 PMC1_HUMAN M-phase inducer phosphatase 1 MPI1_HUMAN DNA topoisomerase II TP2A_HUMAN Cell cycle regulated kinase, inhibits Cdc2 Membrane-associated kinase O14731 Phosphorylated by Cdk2 during S-phase Myb-related protein B MYBB_HUMAN Associated with "growth cones" Brain acid soluble protein 1 BASP_HUMAN Phosphorylated in M-phase Forkhead box protein M1 FXM1_HUMAN High mobility group protein 2 HMG2_HUMAN Cyclin-dependent kinase inhibitor 3 CDN3_HUMAN Mitotic kinesin-like protein 1 Kinesin-like 5 Q8WVP0

29. Questions?