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 Hugo Filtered description Network Comparison Type Value Type Interaction Map red green network_comparison
    Results: HTML CSV LaTeX Showing element 151 to 200 of 8289 in total
    Filtered  : 1
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Rank
    		Hugo
    		description
    		Interaction Map
    		red
    		green
    		network_comparison
    76 NIPSNAP1 nipsnap1 protein. [swissprot;acc:q9bpw8] Low confidence 249.584 226.86 1.10017
    TMEM33 db83 protein. [swissprot;acc:p57088] High confidence 288 362 1.25694
    77 no value putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Low confidence 195.851 215.424 1.09994
    CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] High confidence 254.692 202.668 1.2567
    78 CACNG8 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 254.693
    LENG4 malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Low confidence 211 231.635 1.0978
    79 APBA1 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] 229.144 208.803 1.09742
    CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] High confidence 254.693 202.668 1.2567
    80 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 254.691 1.25669
    RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Low confidence 221.194 202.005 1.09499
    81 CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] High confidence 254.614 202.646 1.25645
    TFDP2 transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Low confidence 227.623 208.281 1.09286
    82 DGKH diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] 226.981 208.077 1.09085
    GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence 267.636 335.359 1.25304
    83 DGKD diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Low confidence 226.981 208.077 1.09085
    MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] High confidence 88.2482 110.265 1.24949
    84 no value transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Low confidence 226.338 207.874 1.08882
    MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] High confidence 88.2482 110.265 1.24949
    85 no value melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
    KCND2 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Low confidence 225.735 245.308 1.08671
    86 DFFB dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] 233.922 215.309 1.08645
    MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] High confidence 88.2482 110.265 1.24949
    87 KCND3 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] Low confidence 225.545 244.933 1.08596
    MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] High confidence 88.2482 110.265 1.24949
    88 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
    KCND1 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Low confidence 225.428 244.701 1.0855
    89 MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] High confidence 88.2482 110.265 1.24949
    STARD7 star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Low confidence 228.743 210.764 1.0853
    90 NDN necdin. [swissprot;acc:q99608] High confidence 88.2482 110.265 1.24949
    TAF2 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] Low confidence 237.567 219.229 1.08365
    91 MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] High confidence 88.2482 110.265 1.24949
    OPHN1 oligophrenin 1. [swissprot;acc:o60890] Low confidence 233.837 215.973 1.08271
    92 ARHGAP26 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] 233.592 215.846 1.08222
    MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] High confidence 88.2482 110.265 1.24949
    93 DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Low confidence 247.334 228.84 1.08082
    MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] High confidence 88.2482 110.265 1.24949
    94 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Low confidence 247.087 228.693 1.08043
    95 MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] High confidence 88.2482 110.265 1.24949
    SLC7A13 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] Low confidence 200.497 185.679 1.0798
    96 MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] High confidence 88.2482 110.265 1.24949
    SLC7A7 y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] Low confidence 200.497 185.679 1.0798
    97 MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] High confidence 88.2482 110.265 1.24949
    SLC7A11 cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Low confidence 200.497 185.679 1.0798
    98 MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] High confidence 88.2482 110.265 1.24949
    SLC7A6 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Low confidence 200.497 185.679 1.0798
    99 no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] High confidence 88.2482 110.265 1.24949
    EIF4B eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Low confidence 200.497 185.679 1.0798
    100 MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] High confidence 88.2482 110.265 1.24949
    SLC7A9 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Low confidence 200.497 185.679 1.0798

    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/