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 Hugo Value Type description Rank Interaction Map Network Comparison Type green Filtered network_comparison red
    Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
    Hugo  : no value
    Value Type  : Ranked
    Interaction Map  : High confidence
    Network Comparison Type  : Divided
    Filtered  : 1
    description
    		Rank
    		green
    		network_comparison
    		red
    1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 1038 181.041 1.03148 186.741
    15 kda selenoprotein precursor. [swissprot;acc:o60613] 1948 212.432 1.00984 214.522
    17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 1051 217.998 1.03097 211.449
    26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 2316 218.311 1.00493 217.241
    3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 2756 0.00001 1 0.00001
    3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] 2802
    3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 1852 198.154 1.01095 196.008
    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 222.215 1.01272 219.423
    40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 304 266.986 1.1017 242.339
    40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 387 264.11 1.09029 242.238
    40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 344 265.136 1.0973 241.625
    40s ribosomal protein s26. [swissprot;acc:p02383] 454 226.578 1.07779 210.224
    40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 1102 235.974 1.02847 229.442
    40s ribosomal protein s28. [swissprot;acc:p25112] 1982 198.427 1.00966 200.343
    40s ribosomal protein s29. [swissprot;acc:p30054] 277 267.642 1.10665 241.849
    40s ribosomal protein s3a. [swissprot;acc:p49241] 867 234.674 1.03981 225.689
    40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 288 266.078 1.10517 240.758
    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] 789 234.511 1.04578 224.244
    60s acidic ribosomal protein p1. [swissprot;acc:p05386] 898 238.048 1.03874 229.171
    60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 357 266.661 1.09683 243.12
    60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 356 266.796 1.09684 243.24
    60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 338 267.528 1.0983 243.583
    60s ribosomal protein l12. [swissprot;acc:p30050] 337 267.527
    60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 306 266.673 1.10126 242.153
    60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 281 267.335 1.10557 241.808
    60s ribosomal protein l18a. [swissprot;acc:q02543] 860 224.958 1.04031 234.025
    60s ribosomal protein l21. [swissprot;acc:p46778] 1054 217.263 1.03082 223.958
    60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 2205 200.413 1.00645 199.129
    60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 293 265.717 1.10356 240.782
    60s ribosomal protein l23a. [swissprot;acc:p29316] 323 265.945 1.09947 241.884
    60s ribosomal protein l37a. [swissprot;acc:p12751] 2959 0.00001 1 0.00001
    60s ribosomal protein l39. [swissprot;acc:p02404] 859 224.958 1.04031 234.025
    60s ribosomal protein l7. [swissprot;acc:p18124] 297 259.984 1.1029 235.727
    60s ribosomal protein l9. [swissprot;acc:p32969] 341 263.798 1.09805 240.243
    acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 2019 213.865 1.00904 215.799
    adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 1595 225.731 1.01619 222.134
    adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367] 2046 198.24 1.00851 199.928
    adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 1049 217.998 1.03097 211.449
    adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 348 265.696 1.09728 242.14
    adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 1186 212.904 1.02582 218.402
    alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 2428 193.555 1.00355 192.871
    alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 1189 204.406 1.02565 209.649
    alpha-nac protein. [sptrembl;acc:q9h009] 889 204.053 1.03908 212.028
    alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 1249 224.7 1.02437 219.354
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 248 212.41 1.11719 237.302
    apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 1111 212.123 1.02766 217.99
    arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] 2291 201.213 1.00527 200.158
    aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 658 216.576 1.0577 229.072
    ataxin 2-binding protein. [swissprot;acc:q9nwb1] 1704 215.577 1.01362 218.514
    ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 1059 221.293 1.03078 228.105

    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/