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 Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 125 to 174 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    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 High confidence 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] 950 SRD5A2 Low confidence 204.147 199.196 1.02485
    1084 High confidence 220.118 213.685 1.03011
    3-oxo-5-beta-steroid 4-dehydrogenase (ec 1.3.99.6) (delta(4)-3- ketosteroid 5-beta-reductase) (aldo-keto reductase family 1 member d1). [swissprot;acc:p51857] 1902 AKR1D1 Low confidence 201.286 197.384 1.01977
    3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] 897 PDPK1 High confidence 272.878 283.472 1.03882
    4765 Low confidence 206.842 205.83 1.00492
    38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318] 2068 FKBP8 203.696 207.631 1.01932
    2358 High confidence 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
    2696 Low confidence 196.941 193.541 1.01757
    4-hydroxyphenylpyruvate dioxygenase (ec 1.13.11.27) (4hppd) (hpd) (hppdase). [swissprot;acc:p32754] 1159 HPD 203.422 198.786 1.02332
    40 kda peptidyl-prolyl cis-trans isomerase (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin-40) (cyp-40) (cyclophilin-related protein). [swissprot;acc:q08752] 3251 PPID 197.955 194.871 1.01583
    40s ribosomal protein s10. [swissprot;acc:p46783] 3263 no value 202.739 199.593 1.01576
    40s ribosomal protein s11. [swissprot;acc:p04643] 278 RPS11 High confidence 241.399 267.088 1.10642
    3606 Low confidence 207.913 210.891 1.01432
    40s ribosomal protein s12. [swissprot;acc:p25398] 4261 no value 203.546 201.631 1.0095
    40s ribosomal protein s13. [swissprot;acc:q02546] 1722 RPS13 High confidence 220.899 223.813 1.01319
    3777 Low confidence 201.886 199.227 1.01335
    40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] 386 RPS14 High confidence 242.238 264.11 1.09029
    4717 Low confidence 208.268 209.433 1.00559
    40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 304 no value High confidence 242.339 266.986 1.1017
    4250 Low confidence 207.351 209.342 1.0096
    40s ribosomal protein s15a. [swissprot;acc:p39027] 292 RPS15A High confidence 241.411 266.414 1.10357
    3989 Low confidence 206.934 209.395 1.01189
    40s ribosomal protein s16. [swissprot;acc:p17008] 391 RPS16 High confidence 241.828 263.62 1.09011
    4832 Low confidence 208.276 209.034 1.00364
    40s ribosomal protein s17. [swissprot;acc:p08708] 1630 RPS17L4 204.428 200.265 1.02079
    40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 387 no value High confidence 242.238 264.11 1.09029
    2309 Low confidence 207.747 211.63 1.01869
    40s ribosomal protein s19. [swissprot;acc:p39019] 861 RPS19 High confidence 234.025 224.958 1.04031
    2888 Low confidence 202.851 199.442 1.01709
    40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 344 no value High confidence 241.625 265.136 1.0973
    4600 Low confidence 206.929 208.423 1.00722
    40s ribosomal protein s20. [swissprot;acc:p17075] 342 RPS20 High confidence 243.5 267.21 1.09737
    4957 Low confidence 207.359 207.585 1.00109
    40s ribosomal protein s21. [swissprot;acc:p35265] 790 RPS21 High confidence 224.244 234.511 1.04578
    3794 Low confidence 202.443 199.787 1.01329
    40s ribosomal protein s23. [swissprot;acc:p39028] 324 RPS23 High confidence 243.944 268.195 1.09941
    4531 Low confidence 209.371 211.088 1.0082
    40s ribosomal protein s24 (s19). [swissprot;acc:p16632] 1690 RPS24 High confidence 224.091 227.184 1.0138
    4880 Low confidence 204.152 204.674 1.00256
    40s ribosomal protein s25. [swissprot;acc:p25111] 1980 RPS25 206.198 202.249 1.01953
    40s ribosomal protein s26. [swissprot;acc:p02383] 454 no value High confidence 210.224 226.578 1.07779
    4266 Low confidence 202.198 204.106 1.00944
    40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 1102 High confidence 229.442 235.974 1.02847
    3981 Low confidence 203.072 200.675 1.01194
    40s ribosomal protein s27a. [swissprot;acc:p14798] 3486 RPS27A 202.475 199.484 1.01499
    40s ribosomal protein s28. [swissprot;acc:p25112] 1982 no value High confidence 200.343 198.427 1.00966
    2356 Low confidence 201.372 197.696 1.01859
    40s ribosomal protein s29. [swissprot;acc:p30054] 277 High confidence 241.849 267.642 1.10665

    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/