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 Hugo Rank Gene Value Type Network Comparison Type red Interaction Map Filtered 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
    		Hugo
    		Rank
    		red
    		green
    		network_comparison
    3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035] HMGCR 2303 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] HSD17B10 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] HAAO 2189 209.54 208.162 1.00662
    3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] no value 1852 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] ACAA1 2300 191.563 192.541 1.00511
    3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] MPST 1025 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] SRD5A1 1083 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] SRD5A2 1084
    3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] PDPK1 897 272.878 283.472 1.03882
    38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] FKBP8 2358 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] no value 1745 219.423 222.215 1.01272
    40s ribosomal protein s11. [swissprot;acc:p04643] RPS11 278 241.399 267.088 1.10642
    40s ribosomal protein s13. [swissprot;acc:q02546] RPS13 1722 220.899 223.813 1.01319
    40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] RPS14 386 242.238 264.11 1.09029
    40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] no value 304 242.339 266.986 1.1017
    40s ribosomal protein s15a. [swissprot;acc:p39027] RPS15A 292 241.411 266.414 1.10357
    40s ribosomal protein s16. [swissprot;acc:p17008] RPS16 391 241.828 263.62 1.09011
    40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] no value 387 242.238 264.11 1.09029
    40s ribosomal protein s19. [swissprot;acc:p39019] RPS19 861 234.025 224.958 1.04031
    40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] no value 344 241.625 265.136 1.0973
    40s ribosomal protein s20. [swissprot;acc:p17075] RPS20 342 243.5 267.21 1.09737
    40s ribosomal protein s21. [swissprot;acc:p35265] RPS21 790 224.244 234.511 1.04578
    40s ribosomal protein s23. [swissprot;acc:p39028] RPS23 324 243.944 268.195 1.09941
    40s ribosomal protein s24 (s19). [swissprot;acc:p16632] RPS24 1690 224.091 227.184 1.0138
    40s ribosomal protein s26. [swissprot;acc:p02383] no value 454 210.224 226.578 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] RPS3 346 241.612 265.119 1.09729
    40s ribosomal protein s30. [swissprot;acc:q05472] FAU 1081 223.44 216.875 1.03027
    40s ribosomal protein s3a. [swissprot;acc:p49241] no value 867 225.689 234.674 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] RPS4Y2 287 266.079
    40s ribosomal protein s5. [swissprot;acc:p46782] RPS5 366 242.473 265.756 1.09602
    40s ribosomal protein s7 (s8). [swissprot;acc:p23821] RPS7 2149 217.871 219.366 1.00686
    40s ribosomal protein s8. [swissprot;acc:p09058] RPS8 1397 218.64 214.049 1.02145
    40s ribosomal protein s9. [swissprot;acc:p46781] RPS9 439 238.986 257.784 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] no value 789 224.244 234.511 1.04578
    43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] RAPSN 2232 215.547 214.194 1.00632
    44050 protein. [refseq;acc:nm_178832] C10orf83 2506 151.386 151.009 1.0025
    45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] SDF4 2147 206.442 207.862 1.00688
    5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] PRKAB1 879 212.002 203.954 1.03946
    5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] PRKAB2 877
    5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] PRKAA1 876
    5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] PRKAA2 875
    5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] PRKAG1 874
    5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] PRKAG2 880
    5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] PRKAG3 878
    5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] MTAP 1769 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] TYRP1 1021 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/