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 [...,...].
    Gene description Rank Hugo Value Type Network Comparison Type Interaction Map Filtered red green 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
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] 2303 HMGCR 191.567 192.542 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 HSD17B10 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 HAAO 209.54 208.162 1.00662
    3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 1852 no value 196.008 198.154 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] 2300 ACAA1 191.563 192.541 1.00511
    3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 1025 MPST 205.632 199.266 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 SRD5A1 220.118 213.685 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 SRD5A2
    3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 897 PDPK1 272.878 283.472 1.03882
    38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 2358 FKBP8 198.181 197.346 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] 1745 no value 219.423 222.215 1.01272
    40s ribosomal protein s11. [swissprot;acc:p04643] 278 RPS11 241.399 267.088 1.10642
    40s ribosomal protein s13. [swissprot;acc:q02546] 1722 RPS13 220.899 223.813 1.01319
    40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 386 RPS14 242.238 264.11 1.09029
    40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 304 no value 242.339 266.986 1.1017
    40s ribosomal protein s15a. [swissprot;acc:p39027] 292 RPS15A 241.411 266.414 1.10357
    40s ribosomal protein s16. [swissprot;acc:p17008] 391 RPS16 241.828 263.62 1.09011
    40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 387 no value 242.238 264.11 1.09029
    40s ribosomal protein s19. [swissprot;acc:p39019] 861 RPS19 234.025 224.958 1.04031
    40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 344 no value 241.625 265.136 1.0973
    40s ribosomal protein s20. [swissprot;acc:p17075] 342 RPS20 243.5 267.21 1.09737
    40s ribosomal protein s21. [swissprot;acc:p35265] 790 RPS21 224.244 234.511 1.04578
    40s ribosomal protein s23. [swissprot;acc:p39028] 324 RPS23 243.944 268.195 1.09941
    40s ribosomal protein s24 (s19). [swissprot;acc:p16632] 1690 RPS24 224.091 227.184 1.0138
    40s ribosomal protein s26. [swissprot;acc:p02383] 454 no value 210.224 226.578 1.07779
    40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 1102 229.442 235.974 1.02847
    40s ribosomal protein s28. [swissprot;acc:p25112] 1982 200.343 198.427 1.00966
    40s ribosomal protein s29. [swissprot;acc:p30054] 277 241.849 267.642 1.10665
    40s ribosomal protein s3. [swissprot;acc:p23396] 346 RPS3 241.612 265.119 1.09729
    40s ribosomal protein s30. [swissprot;acc:q05472] 1081 FAU 223.44 216.875 1.03027
    40s ribosomal protein s3a. [swissprot;acc:p49241] 867 no value 225.689 234.674 1.03981
    40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 288 240.758 266.078 1.10517
    40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 287 RPS4Y2 266.079
    40s ribosomal protein s5. [swissprot;acc:p46782] 366 RPS5 242.473 265.756 1.09602
    40s ribosomal protein s7 (s8). [swissprot;acc:p23821] 2149 RPS7 217.871 219.366 1.00686
    40s ribosomal protein s8. [swissprot;acc:p09058] 1397 RPS8 218.64 214.049 1.02145
    40s ribosomal protein s9. [swissprot;acc:p46781] 439 RPS9 238.986 257.784 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] 789 no value 224.244 234.511 1.04578
    43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 2232 RAPSN 215.547 214.194 1.00632
    44050 protein. [refseq;acc:nm_178832] 2506 C10orf83 151.386 151.009 1.0025
    45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] 2147 SDF4 206.442 207.862 1.00688
    5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 879 PRKAB1 212.002 203.954 1.03946
    5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 877 PRKAB2
    5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 876 PRKAA1
    5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 875 PRKAA2
    5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 874 PRKAG1
    5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 880 PRKAG2
    5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 878 PRKAG3
    5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] 1769 MTAP 223.016 225.734 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] 1021 TYRP1 221.278 214.409 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
    - Hugo is the HGNC identifier if it exists
    - 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/