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 [...,...].
    Value Type description Gene green Rank Network Comparison Type Interaction Map Filtered red network_comparison
    Results: HTML CSV LaTeX Showing element 51 to 100 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		green
    		Rank
    		red
    		network_comparison
    3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] 192.542 2303 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] 0.00001 3180 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] 208.162 2189 209.54 1.00662
    3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 198.154 1852 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] 192.541 2300 191.563 1.00511
    3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 199.266 1025 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] 213.685 1083 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] 283.472 897 272.878 1.03882
    38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 197.346 2358 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] 222.215 1745 219.423 1.01272
    40s ribosomal protein s11. [swissprot;acc:p04643] 267.088 278 241.399 1.10642
    40s ribosomal protein s13. [swissprot;acc:q02546] 223.813 1722 220.899 1.01319
    40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 264.11 386 242.238 1.09029
    40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 266.986 304 242.339 1.1017
    40s ribosomal protein s15a. [swissprot;acc:p39027] 266.414 292 241.411 1.10357
    40s ribosomal protein s16. [swissprot;acc:p17008] 263.62 391 241.828 1.09011
    40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 264.11 387 242.238 1.09029
    40s ribosomal protein s19. [swissprot;acc:p39019] 224.958 861 234.025 1.04031
    40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 265.136 344 241.625 1.0973
    40s ribosomal protein s20. [swissprot;acc:p17075] 267.21 342 243.5 1.09737
    40s ribosomal protein s21. [swissprot;acc:p35265] 234.511 790 224.244 1.04578
    40s ribosomal protein s23. [swissprot;acc:p39028] 268.195 324 243.944 1.09941
    40s ribosomal protein s24 (s19). [swissprot;acc:p16632] 227.184 1690 224.091 1.0138
    40s ribosomal protein s26. [swissprot;acc:p02383] 226.578 454 210.224 1.07779
    40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 235.974 1102 229.442 1.02847
    40s ribosomal protein s28. [swissprot;acc:p25112] 198.427 1982 200.343 1.00966
    40s ribosomal protein s29. [swissprot;acc:p30054] 267.642 277 241.849 1.10665
    40s ribosomal protein s3. [swissprot;acc:p23396] 265.119 346 241.612 1.09729
    40s ribosomal protein s30. [swissprot;acc:q05472] 216.875 1081 223.44 1.03027
    40s ribosomal protein s3a. [swissprot;acc:p49241] 234.674 867 225.689 1.03981
    40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 266.078 288 240.758 1.10517
    40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 266.079 287
    40s ribosomal protein s5. [swissprot;acc:p46782] 265.756 366 242.473 1.09602
    40s ribosomal protein s7 (s8). [swissprot;acc:p23821] 219.366 2149 217.871 1.00686
    40s ribosomal protein s8. [swissprot;acc:p09058] 214.049 1397 218.64 1.02145
    40s ribosomal protein s9. [swissprot;acc:p46781] 257.784 439 238.986 1.07866
    40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 234.511 789 224.244 1.04578
    43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 214.194 2232 215.547 1.00632
    44050 protein. [refseq;acc:nm_178832] 151.009 2506 151.386 1.0025
    45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 207.862 2147 206.442 1.00688
    5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 203.954 879 212.002 1.03946
    5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 877
    5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 876
    5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 875
    5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 874
    5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 880
    5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 878
    5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 225.734 1769 223.016 1.01219
    5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 214.409 1021 221.278 1.03204

    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/