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 [...,...].
    Filtered Gene Value Type Network Comparison Type Rank description Interaction Map network_comparison green red
    Results: HTML CSV LaTeX Showing element 51 to 100 of 77072 in total
    Filtered  : 0
    Value Type  : Measured
    Network Comparison Type  : Divided
    Rank
    		description
    		Interaction Map
    		network_comparison
    		green
    		red
    26 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] High confidence 4.3268 662 153
    glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Low confidence 3.04255 47 143
    27 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 2.97183 35.5 105.5
    phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] High confidence 4.10072 139 570
    28 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Low confidence 2.97183 35.5 105.5
    29 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] High confidence 3.90833 434.911 111.278
    30 dystrophin. [swissprot;acc:p11532] 3.82335 111.739 427.217
    melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Low confidence 2.97183 35.5 105.5
    31 dok-like protein. [refseq;acc:nm_024872] High confidence 3500000 0.00001 35
    hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Low confidence 2.97183 35.5 105.5
    32 cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] High confidence 3.25 184 598
    melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Low confidence 2.97183 35.5 105.5
    33 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] High confidence 3.15402 39.8063 12.6208
    melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Low confidence 2.97183 35.5 105.5
    34 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] High confidence 3.04255 47 143
    melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Low confidence 2.97183 35.5 105.5
    35 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] High confidence 2.99674 1377 459.5
    melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Low confidence 2.97183 35.5 105.5
    36 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] High confidence 2.80357 56 157
    melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Low confidence 2.97183 35.5 105.5
    37 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 2.79409 934.348 334.401
    melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Low confidence 2.97183 35.5 105.5
    38 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
    zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] High confidence 2.65727 120.429 320.012
    39 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Low confidence 2.97183 35.5 105.5
    microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] High confidence 2.50878 192.295 482.426
    40 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Low confidence 2.97183 35.5 105.5
    nanos (fragment). [sptrembl;acc:q8wy41] High confidence 2.49669 151 377
    41 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Low confidence 2.97183 35.5 105.5
    nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] High confidence 2.42481 645 266
    42 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Low confidence 2.97183 35.5 105.5
    presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] High confidence 2.36266 86.9525 205.439
    43 elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] 2.2301 587.988 263.66
    melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Low confidence 2.97183 35.5 105.5
    44 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] High confidence 2.16837 98.5074 45.4292
    neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Low confidence 28600000 0.00001 286
    45 neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
    tigger transposable element derived 6. [refseq;acc:nm_030953] High confidence 2.1673 438.605 202.374
    46 ephrin type-b receptor 4 precursor (ec 2.7.1.112) (tyrosine-protein kinase receptor htk). [swissprot;acc:p54760] Low confidence 2.79167 67 24
    tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] High confidence 2.16674 438.035 202.163
    47 tenascin-x precursor (tn-x) (hexabrachion-like). [swissprot;acc:p22105] Low confidence 2.50526 776.89 310.103
    tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] High confidence 2.16672 438.016 202.156
    48 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 2.15895 403.196 870.482
    pnas-129. [sptrembl;acc:q9bxv8] Low confidence 2.42708 151.073 366.666
    49 nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 2.42481 645 266
    selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] High confidence 2.09722 151 72
    50 latrophilin 2; lectomedin-1; latrophilin homolog 2 (cow). [refseq;acc:nm_012302] Low confidence 2.36036 111 262
    transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] High confidence 2.09524 21 44

    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/