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 Network Comparison Type description Hugo Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 132 to 181 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    66 mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] MTUS1 Low confidence 221.902 200.783 1.10518
    67 guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] GNAT2 High confidence 267.14 336.075 1.25805
    retinoblastoma-associated factor 600. [refseq;acc:nm_020765] UBR4 Low confidence 165.535 149.799 1.10505
    68 60s ribosomal protein l37a. [swissprot;acc:p12751] no value 239.692 217.005 1.10455
    guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] GNAZ High confidence 267.139 336.075 1.25805
    69 guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] GNAT1 267.14
    testis-specific protein tex28. [swissprot;acc:o15482] TEX28P2 Low confidence 259.517 235.017 1.10425
    70 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653] GOSR2
    guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] GNAI2 High confidence 267.142 336.074 1.25804
    71 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] no value Low confidence 230.944 209.149 1.10421
    guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] GNAI1 High confidence 267.144 336.073 1.25802
    72 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] GNAI3
    set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] SMYD2 Low confidence 230.944 209.149 1.10421
    73 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] JPH3 High confidence 288 362 1.25694
    set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] SMYD1 Low confidence 230.944 209.149 1.10421
    74 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] JPH2 High confidence 288 362 1.25694
    putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] AHCYL1 Low confidence 195.817 215.516 1.1006
    75 nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] GBAS 249.709 226.944 1.10031
    sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] SMPD2 High confidence 288 362 1.25694
    76 db83 protein. [swissprot;acc:p57088] TMEM33
    nipsnap1 protein. [swissprot;acc:q9bpw8] NIPSNAP1 Low confidence 249.584 226.86 1.10017
    77 putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] no value 195.851 215.424 1.09994
    voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] CACNG2 High confidence 254.692 202.668 1.2567
    78 malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] LENG4 Low confidence 211 231.635 1.0978
    voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] CACNG8 High confidence 254.693 202.668 1.2567
    79 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] APBA1 Low confidence 229.144 208.803 1.09742
    voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] CACNG3 High confidence 254.693 202.668 1.2567
    80 rad50-interacting protein 1. [refseq;acc:nm_021930] RINT1 Low confidence 221.194 202.005 1.09499
    voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] CACNG4 High confidence 254.691 202.668 1.25669
    81 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] TFDP2 Low confidence 227.623 208.281 1.09286
    voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] CACNG5 High confidence 254.614 202.646 1.25645
    82 diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] DGKH Low confidence 226.981 208.077 1.09085
    guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] GNB5 High confidence 267.636 335.359 1.25304
    83 diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] DGKD Low confidence 226.981 208.077 1.09085
    melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] MAGED4 High confidence 88.2482 110.265 1.24949
    84 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] MAGEE2
    transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] no value Low confidence 226.338 207.874 1.08882
    85 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] High confidence 88.2482 110.265 1.24949
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] KCND2 Low confidence 225.735 245.308 1.08671
    86 dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] DFFB 233.922 215.309 1.08645
    melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] MAGEA11 High confidence 88.2482 110.265 1.24949
    87 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] MAGEA2B
    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] KCND3 Low confidence 225.545 244.933 1.08596
    88 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] no value High confidence 88.2482 110.265 1.24949
    potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] KCND1 Low confidence 225.428 244.701 1.0855
    89 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] MAGEA6 High confidence 88.2482 110.265 1.24949
    star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] STARD7 Low confidence 228.743 210.764 1.0853
    90 necdin. [swissprot;acc:q99608] NDN High confidence 88.2482 110.265 1.24949
    tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] TAF2 Low confidence 237.567 219.229 1.08365
    91 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] MAGED1 High confidence 88.2482 110.265 1.24949

    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/