Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    description Rank Gene Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
    Results: HTML CSV LaTeX Showing element 51 to 100 of 3730 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    description
    		Rank
    		Filtered
    		green
    		red
    		network_comparison
    28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 407 1 260.544 239.75 1.08673
    3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193] 3147 0.00001 0.00001 1
    3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 299 0 11512.3 12338.7 1.07178
    2756 1 0.00001 0.00001 1
    3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] 2802
    3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] 2303 192.542 191.567 1.00509
    3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714] 3180 0.00001 0.00001 1
    3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] 2189 208.162 209.54 1.00662
    3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 327 0 10466.5 9897.29 1.05751
    1852 1 198.154 196.008 1.01095
    3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 478 0 10243.1 10156.4 1.00854
    2300 1 192.541 191.563 1.00511
    3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 1025 199.266 205.632 1.03195
    3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] 1083 213.685 220.118 1.03011
    3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] 1084
    3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 897 283.472 272.878 1.03882
    38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 2358 197.346 198.181 1.00423
    4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 369 0 19704.7 18849.7 1.04536
    1745 1 222.215 219.423 1.01272
    40s ribosomal protein s11. [swissprot;acc:p04643] 278 267.088 241.399 1.10642
    40s ribosomal protein s13. [swissprot;acc:q02546] 1722 223.813 220.899 1.01319
    40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 386 264.11 242.238 1.09029
    40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 222 0 11013.2 12183 1.10622
    304 1 266.986 242.339 1.1017
    40s ribosomal protein s15a. [swissprot;acc:p39027] 292 266.414 241.411 1.10357
    40s ribosomal protein s16. [swissprot;acc:p17008] 391 263.62 241.828 1.09011
    40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 387 264.11 242.238 1.09029
    40s ribosomal protein s19. [swissprot;acc:p39019] 861 224.958 234.025 1.04031
    40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 186 0 10592.8 11935.1 1.12672
    344 1 265.136 241.625 1.0973
    40s ribosomal protein s20. [swissprot;acc:p17075] 342 267.21 243.5 1.09737
    40s ribosomal protein s21. [swissprot;acc:p35265] 790 234.511 224.244 1.04578
    40s ribosomal protein s23. [swissprot;acc:p39028] 324 268.195 243.944 1.09941
    40s ribosomal protein s24 (s19). [swissprot;acc:p16632] 1690 227.184 224.091 1.0138
    40s ribosomal protein s26. [swissprot;acc:p02383] 112 0 17098 14269.7 1.1982
    454 1 226.578 210.224 1.07779
    40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 380 0 9936.37 9566.15 1.0387
    1102 1 235.974 229.442 1.02847
    40s ribosomal protein s28. [swissprot;acc:p25112] 258 0 14193.6 12967.1 1.09459
    1982 1 198.427 200.343 1.00966
    40s ribosomal protein s29. [swissprot;acc:p30054] 225 0 9997.71 11035.3 1.10378
    277 1 267.642 241.849 1.10665
    40s ribosomal protein s3. [swissprot;acc:p23396] 346 265.119 241.612 1.09729
    40s ribosomal protein s30. [swissprot;acc:q05472] 1081 216.875 223.44 1.03027
    40s ribosomal protein s3a. [swissprot;acc:p49241] 331 0 10992.4 10405.1 1.05644
    867 1 234.674 225.689 1.03981
    40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 261 0 11393.9 12448.9 1.09259
    288 1 266.078 240.758 1.10517
    40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 260 0 11392.6 12447.6 1.0926
    287 1 266.079 240.758 1.10517

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/