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 description Hugo Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 2075 to 2124 of 25824 in total
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		Value Type
    		red
    		network_comparison
    		green
    260 huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] HIP1R Divided Squared 76296.4 1.29752 58801.6
    multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] SCYE1 Rooted 59.0951 1.12417 66.4332
    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] SH3GL1 Subtracted Squared 35793 8802.3 44595.3
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 Divided Measured 4244.95 1.22343 5193.42
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Subtracted Rooted 56.7592 9.2297 65.9889
    surfeit locus protein 5. [swissprot;acc:q15528] MED22 Ranked 242.14 23.556 265.696
    261 carboxypeptidase a5. [refseq;acc:nm_080385] CPA5 Squared 53174 8796.6 44377.4
    eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] EIF4G3 Rooted 52.7582 9.1541 61.9123
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] HS3ST3A1 Divided Ranked 219.421 1.11394 196.978
    pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] PC Squared 48127.9 1.29334 62245.6
    ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B Rooted 62.3337 1.12417 70.0738
    signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] SRP9 Measured 4247.36 1.22255 5192.61
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Subtracted 4571.89 1292.97 5864.86
    zinc finger protein 291. [swissprot;acc:q9by12] SCAPER Ranked 242.14 23.556 265.696
    262 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] CPB1 Squared 53174 8796.6 44377.4
    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] CPSF4 Divided Measured 24896.4 1.21852 20431.7
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] HS3ST3B1 Ranked 219.421 1.11394 196.978
    neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] CHRNA7 Squared 26157.6 1.29261 20236.2
    oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] STT3A Subtracted Measured 4571.89 1292.97 5864.86
    peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] PEX1 Ranked 242.14 23.556 265.696
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] POLI Divided Rooted 59.4073 1.12276 66.7002
    rna-binding protein. [refseq;acc:nm_019027] no value Subtracted 52.7642 9.1377 61.9019
    263 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] ADCY6 Divided Squared 26157.6 1.29261 20236.2
    apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] no value Subtracted Rooted 52.7642 9.1377 61.9019
    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] DDOST Measured 4571.89 1292.97 5864.86
    heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] HS3ST2 Divided Ranked 219.421 1.11394 196.978
    neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] SLC3A1 Subtracted Squared 53174 8796.6 44377.4
    paxillin. [swissprot;acc:p49023] PXN Divided Rooted 59.4073 1.12276 66.7002
    protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] TXNDC9 Subtracted Ranked 242.14 23.556 265.696
    trs85 homolog. [swissprot;acc:q9y2l5] KIAA1012 Divided Measured 24896.4 1.21852 20431.7
    264 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] no value Subtracted Ranked 243.24 23.556 266.796
    adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] ADCY5 Divided Squared 26157.6 1.29261 20236.2
    aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] ACY1 Subtracted 53174 8796.6 44377.4
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 Divided Measured 4987.58 1.2181 4094.57
    ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] CTPS Subtracted 12503.3 1291.3 11212
    mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] DCPS Divided Ranked 219.421 1.11394 196.978
    ns1-associated protein 1. [refseq;acc:nm_006372] SYNCRIP Subtracted Rooted 52.7642 9.1377 61.9019
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] WAS Divided 66.1122 1.12148 74.1438
    265 60s ribosomal protein l9. [swissprot;acc:p32969] no value Subtracted Ranked 240.243 23.555 263.798
    carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] CPA1 Squared 53174 8796.6 44377.4
    heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] HNRNPR Rooted 52.7642 9.1377 61.9019
    leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] LRRC15 Divided Squared 26157.6 1.29261 20236.2
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Ranked 225.217 1.11241 202.459
    Subtracted Measured 4638.1 1285.3 5923.4
    u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] LSM8 Divided Rooted 56.031 1.12131 62.8281
    wd-repeat protein wdc146. [swissprot;acc:q9c0j8] WDR33 Measured 24806.9 1.21782 20369.9
    266 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] CPSF1
    eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] EIF4G1 Subtracted Rooted 52.7702 9.1213 61.8915
    fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] FEM1B Divided Squared 26157.6 1.29261 20236.2
    heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] HNRNPL Subtracted 59335 8727.6 68062.6

    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/