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 Value Type Network Comparison Type description Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2062 to 2111 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		Network Comparison Type
    		description
    		red
    		green
    		network_comparison
    258 PAPOLG Rooted Subtracted poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 132.063 122.761 9.302
    RAB24 Measured max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 4457.06 5773.63 1316.57
    THBS3 Rooted Divided thrombospondin 3 precursor. [swissprot;acc:p49746] 51.6132 45.8422 1.12589
    259 no value Ranked Subtracted adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 242.14 265.696 23.556
    Squared nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] 33514.4 42370.8 8856.4
    COL4A3BP Divided goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] 76360.8 58841.7 1.29773
    RAB24 Ranked max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 227.999 204.37 1.11562
    SEPT4 Rooted Subtracted septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 107.961 117.197 9.236
    SNRPD3 Measured small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 4569.48 5885.79 1316.31
    TFIP11 Rooted Divided tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 58.2964 65.5926 1.12516
    WASL Measured neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 6417.81 7852.52 1.22355
    260 CTPS2 Subtracted cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 12515.4 11221.1 1294.3
    HIP1R Squared Divided huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 76296.4 58801.6 1.29752
    HS3ST6 Ranked c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 219.421 196.978 1.11394
    MED22 Subtracted surfeit locus protein 5. [swissprot;acc:q15528] 242.14 265.696 23.556
    SCYE1 Rooted Divided multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 59.0951 66.4332 1.12417
    SF3B1 Subtracted splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 56.7592 65.9889 9.2297
    SH3GL1 Squared sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 35793 44595.3 8802.3
    SRP9 Measured Divided signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 4244.95 5193.42 1.22343
    261 CPA5 Squared Subtracted carboxypeptidase a5. [refseq;acc:nm_080385] 53174 44377.4 8796.6
    EIF4G3 Rooted eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 52.7582 61.9123 9.1541
    HS3ST3A1 Ranked Divided heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 219.421 196.978 1.11394
    PC Squared pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] 48127.9 62245.6 1.29334
    RRM2B Rooted ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 62.3337 70.0738 1.12417
    SCAPER Ranked Subtracted zinc finger protein 291. [swissprot;acc:q9by12] 242.14 265.696 23.556
    SRP9 Measured Divided signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 4247.36 5192.61 1.22255
    STT3B Subtracted source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 4571.89 5864.86 1292.97
    262 no value Rooted rna-binding protein. [refseq;acc:nm_019027] 52.7642 61.9019 9.1377
    CHRNA7 Squared Divided neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 26157.6 20236.2 1.29261
    CPB1 Subtracted carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 53174 44377.4 8796.6
    CPSF4 Measured Divided cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 24896.4 20431.7 1.21852
    HS3ST3B1 Ranked heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 219.421 196.978 1.11394
    PEX1 Subtracted peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 242.14 265.696 23.556
    POLI Rooted Divided polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 59.4073 66.7002 1.12276
    STT3A Measured Subtracted oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 4571.89 5864.86 1292.97
    263 no value Rooted apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 52.7642 61.9019 9.1377
    ADCY6 Squared Divided adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 26157.6 20236.2 1.29261
    DDOST Measured Subtracted dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 4571.89 5864.86 1292.97
    HS3ST2 Ranked Divided heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 219.421 196.978 1.11394
    KIAA1012 Measured trs85 homolog. [swissprot;acc:q9y2l5] 24896.4 20431.7 1.21852
    PXN Rooted paxillin. [swissprot;acc:p49023] 59.4073 66.7002 1.12276
    SLC3A1 Squared Subtracted neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] 53174 44377.4 8796.6
    TXNDC9 Ranked protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 242.14 265.696 23.556
    264 no value 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796
    ACY1 Squared aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] 53174 44377.4 8796.6
    ADCY5 Divided adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 26157.6 20236.2 1.29261
    COPS3 Measured cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 4987.58 4094.57 1.2181
    CTPS Subtracted ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 12503.3 11212 1291.3
    DCPS Ranked Divided mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 219.421 196.978 1.11394
    SYNCRIP Rooted Subtracted ns1-associated protein 1. [refseq;acc:nm_006372] 52.7642 61.9019 9.1377

    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/