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 Network Comparison Type description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 5908 to 5957 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		Network Comparison Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    1477 RTN3 Subtracted reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] High confidence 207.013 4.037 211.05
    1478 SFRS10 Divided arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] 215.122 1.01922 211.066
    TBX1 t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435] Low confidence 198.794 1.02151 194.608
    TRIP12 Subtracted thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] High confidence 205.817 4.034 209.851
    ZNF259 zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Low confidence 203.346 4.238 199.108
    1479 DLSTP dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] High confidence 205.817 4.034 209.851
    HLTF swi/snf-related matrix-associated actin-dependent regulator of chromatin a3; snf2-like 3; helicase-like transcription factor; dna-binding protein/plasminogen activator inhibitor-1 regulator; sucrose nonfermenting-like 3. [refseq;acc:nm_003071] Low confidence 202.287 4.237 198.05
    MPP6 Divided maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] High confidence 228.469 1.0192 232.855
    UBE2S ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763] Low confidence 198.794 1.02151 194.608
    1480 CPSF6 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] High confidence 218.664 1.01918 214.55
    MAP3K7 Subtracted mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] 213.251 3.987 209.264
    RXRG Divided retinoic acid receptor rxr-gamma. [swissprot;acc:p48443] Low confidence 203.213 1.0215 198.935
    UTY Subtracted ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 200.929 4.236 196.693
    1481 ACTR1A alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024] High confidence 225.148 3.971 221.177
    CDC23 Divided cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 208.432 1.01915 204.516
    SFRS18 sr rich protein. [refseq;acc:nm_032870] Low confidence 204.229 1.0215 199.931
    UTX Subtracted ubiquitously transcribed x chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the x chromosome). [swissprot;acc:o15550] 200.93 4.236 196.694
    1482 no value Divided retinoic acid receptor rxr-beta. [swissprot;acc:p28702] 203.213 1.0215 198.936
    ACTR1B Subtracted beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025] High confidence 225.148 3.971 221.177
    LSAMP Divided limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 224.354 1.0191 220.15
    PYCR2 Subtracted pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Low confidence 197.57 4.236 193.334
    1483 no value huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 201.541 4.235 197.306
    LETMD1 Divided cervical cancer 1 protooncogene protein p40; regulator of tp53. [refseq;acc:nm_015416] 204.229 1.0215 199.931
    PDHB pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] High confidence 198.927 1.0191 202.726
    RBM10 Subtracted rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] 228.419 3.957 232.376
    1484 ALDH1B1 Divided aldehyde dehydrogenase x, mitochondrial precursor (ec 1.2.1.3) (aldh class 2). [swissprot;acc:p30837] Low confidence 205.089 1.02148 209.494
    CYCS Subtracted cytochrome c. [swissprot;acc:p00001] High confidence 228.419 3.957 232.376
    FH fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Low confidence 201.541 4.235 197.306
    TMEM91 Divided 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] High confidence 198.927 1.0191 202.726
    1485 AIFM2 Subtracted apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] Low confidence 200.475 4.235 196.24
    ARHGAP1 Divided rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960] 205.448 1.02146 201.131
    HS6ST2 Subtracted heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] High confidence 228.419 3.957 232.376
    RBPJ Divided j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 207.877 1.01906 203.989
    1486 no value huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Low confidence 201.541 1.02146 197.306
    HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] High confidence 207.877 1.01906 203.989
    HS6ST1 Subtracted heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] 228.419 3.957 232.376
    PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Low confidence 197.603 4.228 193.375
    1487 CCNH Divided cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 201.236 1.02146 197.009
    FA2H Subtracted fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] High confidence 228.419 3.957 232.376
    HIVEP1 Divided zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] 207.877 1.01906 203.989
    MTHFD1 Subtracted c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] Low confidence 203.321 4.228 199.093
    1488 CCNH cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 201.236 4.227 197.009
    FH Divided fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] 201.541 1.02146 197.306
    HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] High confidence 207.877 1.01906 203.989
    WBP11 Subtracted ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] 228.419 3.957 232.376
    1489 AKAP5 a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588] Low confidence 206.235 4.226 202.009
    ELAC2 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] High confidence 228.419 3.957 232.376
    ELAVL1 Divided elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Low confidence 202.955 1.02146 198.692
    MAP3K7 mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318] High confidence 213.251 1.01905 209.264
    1490 BCCIP brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Low confidence 202.583 1.02145 198.329

    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/