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 [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 968 to 1017 of 29840 in total
    Interaction Map  : High confidence
    Rank
    		description
    		Value Type
    		Network Comparison Type
    		Filtered
    		red
    		green
    		network_comparison
    61 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Rooted Subtracted 1 137.446 120.823 16.623
    muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 0 15.7225 22.5496 6.8271
    necdin. [swissprot;acc:q99608] Squared Divided 1 219048 129762 1.68808
    peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Subtracted 0 8107.36 10981.2 2873.84
    potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Ranked 1 269.248 327.642 58.394
    selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 0 14463 11356 3107
    testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Divided 15352 11346.5 1.35302
    transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] Rooted 6.63325 4.58258 1.44749
    type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] Squared Subtracted 1 192779 126095 66684
    62 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] Ranked 0 17410.5 14360 3050.5
    beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured 1 6475.5 10307.5 3832
    bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] Rooted Divided 0 15.0883 21.8314 1.44691
    Subtracted 6.7431
    dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Measured Divided 210.767 384.407 1.82385
    elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Squared 21.2079 6.15501 3.44563
    glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Ranked 9418.7 12695.6 1.34791
    glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured 1 4489.19 2765.82 1.6231
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 266.865 336.181 1.25974
    melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Rooted Subtracted 137.446 120.823 16.623
    melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared Divided 219048 129762 1.68808
    pnas-18. [sptrembl;acc:q9bzu3] Subtracted 0 14643.9 11814.6 2829.3
    potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Rooted Divided 1 43.4519 31.7522 1.36847
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Ranked Subtracted 269.23 327.601 58.371
    putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Measured 0 1442 977 465
    ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 1 189976 124480 65496
    63 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted Divided 0 18.1049 12.6095 1.43581
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked 1 266.865 336.178 1.25973
    kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Rooted 43.4554 31.7576 1.36835
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 137.446 120.823 16.623
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared Divided 219048 129762 1.68808
    myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured 4489.19 2765.82 1.6231
    nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Ranked Subtracted 260.532 204.309 56.223
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided 0 8519.83 11453 1.34428
    phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Measured Subtracted 1442 977 465
    protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared Divided 1.24091 0.365145 3.3984
    putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Rooted Subtracted 37.9737 31.257 6.7167
    ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Squared 99229.9 96418.4 2811.5
    serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] 1 189976 124480 65496
    spermatogenesis associated 6. [refseq;acc:nm_019073] Measured 6475.5 10307.5 3832
    spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Divided 0 31.1429 56.278 1.80709
    Ranked Subtracted 18662.8 15627 3035.8
    64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted Divided 1 63.8686 47.2654 1.35128
    amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Measured Subtracted 6475.5 10307.5 3832
    ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Ranked 260.532 204.309 56.223
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Squared 0 14470.6 11676.7 2793.9
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 1 144940 81169.7 63770.3
    glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Measured Divided 4489.19 2765.82 1.6231
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 266.868 336.159 1.25965
    hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Subtracted 0 8152.55 11134.8 2982.25
    importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] Measured 607 1068 461

    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
    - 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/