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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 97 to 146 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 880 PRKAG2 212.002 203.954 1.03946
    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
    5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] 2491 ALAS2 194.527 195.08 1.00284
    5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] 2496 ALAS1
    5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] 2754 MTHFS 210.638 210.642 1.00002
    5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] 1921 MTR 221.607 219.386 1.01012
    54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 2532 NONO 190.405 190.812 1.00214
    6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 1822 PFKL 240.32 243.085 1.01151
    6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 1830 PFKM 243.069 1.01144
    6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] 1883 PFKP 240.317 242.881 1.01067
    6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 2274 PGD 213.642 214.801 1.00542
    6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 1584 PGLS 216.891 220.432 1.01633
    6-pyruvoyl tetrahydrobiopterin synthase (ec 4.2.3.12) (ptps) (ptp synthase). [swissprot;acc:q03393] 2904 PTS 0.00001 0.00001 1
    60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] 2588 HSPD1 222.305 222.64 1.00151
    60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 826 HTATIP 223.186 213.912 1.04335
    60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 1092 RPLP0 226.203 232.855 1.02941
    60s acidic ribosomal protein p1. [swissprot;acc:p05386] 898 no value 229.171 238.048 1.03874
    60s acidic ribosomal protein p2. [swissprot;acc:p05387] 720 RPLP2 231.92 244.435 1.05396
    60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 357 no value 243.12 266.661 1.09683
    60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 356 243.24 266.796 1.09684
    60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 373 MRPL11 242.37 265.255 1.09442
    60s ribosomal protein l11. [swissprot;acc:p39026] 283 RPL11 241.828 267.346 1.10552
    60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 338 no value 243.583 267.528 1.0983
    60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 369 MRPL12 242.159 265.104 1.09475
    60s ribosomal protein l12. [swissprot;acc:p30050] 337 no value 243.583 267.527 1.0983
    60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 390 MRPL13 241.828 263.62 1.09011
    60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 392 RPL13A 241.83 263.615 1.09008
    60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 306 no value 242.153 266.673 1.10126
    60s ribosomal protein l15. [swissprot;acc:p39030] 604 RPL15 217.862 230.978 1.0602
    60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 281 no value 241.808 267.335 1.10557
    60s ribosomal protein l18. [swissprot;acc:q07020] 485 RPL18 237.109 254.667 1.07405
    60s ribosomal protein l18a. [swissprot;acc:q02543] 860 no value 234.025 224.958 1.04031
    60s ribosomal protein l19. [swissprot;acc:p14118] 319 RPL19 240.73 264.729 1.09969
    60s ribosomal protein l21. [swissprot;acc:p46778] 1054 no value 223.958 217.263 1.03082
    60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 2205 199.129 200.413 1.00645
    60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 293 240.782 265.717 1.10356
    60s ribosomal protein l23a. [swissprot;acc:p29316] 323 241.884 265.945 1.09947
    60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 1767 RPL24 201.288 198.86 1.01221
    60s ribosomal protein l26. [swissprot;acc:q02877] 302 RPL26 242.326 267.008 1.10185
    60s ribosomal protein l28. [swissprot;acc:p46779] 1882 RPL28 215.896 213.61 1.0107
    60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] 2664 RPL29 204.768 204.549 1.00107
    60s ribosomal protein l3-like. [swissprot;acc:q92901] 312 RPL3L 242.195 266.663 1.10103
    60s ribosomal protein l30. [swissprot;acc:p04645] 378 RPL30 242.593 265.365 1.09387
    60s ribosomal protein l31. [swissprot;acc:p12947] 862 RPL31 234.025 224.958 1.04031
    60s ribosomal protein l32. [swissprot;acc:p02433] 276 SNORA7A 241.13 266.969 1.10716
    60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] 1333 MRPL34 220.681 215.78 1.02271
    60s ribosomal protein l34. [swissprot;acc:p49207] 308 RPL34 242.153 266.673 1.10126
    60s ribosomal protein l35. [swissprot;acc:p42766] 303 RPL35 242.333 266.999 1.10179

    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/