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 [...,...].
    Gene Rank description Hugo Network Comparison Type red Value Type Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2651 to 2700 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		red
    		Value Type
    		Interaction Map
    		green
    		network_comparison
    332 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 312 Ranked High confidence 284 1.09859
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 14464.3 Squared 18142.8 1.25432
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 5051.16 Measured 5975.51 1.183
    sec14-like protein 2 (alpha-tocopherol associated protein) (tap) (htap) (supernatant protein factor) (spf) (squalene transfer protein). [swissprot;acc:o76054] SEC14L2 9272.87 Low confidence 9795.53 1.05636
    shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] SHROOM3 60.6732 Rooted High confidence 67.2827 1.10894
    zinc finger protein, subfamily 1a, 5; zinc finger transcription factor pegasus. [refseq;acc:nm_022466] IKZF5 50786.2 Squared Low confidence 47088.3 1.07853
    333 l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] LDHA 67.7165 Rooted 71.2378 1.052
    neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1 312 Ranked High confidence 284 1.09859
    nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] PRPF19 5039.63 Measured 5961.83 1.18299
    nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] GTPBP4 49.0526 Rooted 54.3781 1.10857
    nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 14464.3 Squared 18142.8 1.25432
    platelet-activating factor acetylhydrolase ib alpha subunit (ec 3.1.1.47) (paf acetylhydrolase 45 kda subunit) (paf-ah 45 kda subunit) (paf-ah alpha) (pafah alpha) (lissencephaly-1 protein) (lis- 1). [swissprot;acc:p43034] PAFAH1B1 50786.2 Low confidence 47088.3 1.07853
    protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] C20orf43 200.482 Ranked 208.446 1.03972
    vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] ATP6V0A2 8639.75 Measured 9126.51 1.05634
    334 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] CANT1 64975.9 Squared High confidence 81151.2 1.24894
    coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] BICD2 202.616 Ranked Low confidence 194.878 1.03971
    l-lactate dehydrogenase b chain (ec 1.1.1.27) (ldh-b) (ldh heart subunit) (ldh-h). [swissprot;acc:p07195] LDHB 67.7167 Rooted 71.2379 1.052
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4 312 Ranked High confidence 284 1.09859
    nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] no value 49618.3 Squared Low confidence 46012.8 1.07836
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] PLRG1 58.6096 Rooted High confidence 64.9655 1.10844
    sec14-like protein 1. [swissprot;acc:q92503] SEC14L1 9271.66 Measured Low confidence 9793.93 1.05633
    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] SEPT4 14924.4 High confidence 17655.2 1.18298
    335 40s ribosomal protein s11. [swissprot;acc:p04643] RPS11 50.4705 Rooted 45.5342 1.10841
    bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] BICD1 202.616 Ranked Low confidence 194.878 1.03971
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5 312 High confidence 284 1.09859
    clip-associating protein 1; drosophila 'multiple asters' (mast)-like homolog 1. [refseq;acc:nm_015282] CLASP1 67.7167 Rooted Low confidence 71.2379 1.052
    nude nuclear distribution gene e homolog 1 (a. nidulans); lis1-interacting protein nude1, rat homolog. [refseq;acc:nm_017668] NDE1 48994 Squared 45466.4 1.07759
    probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] DDX56 3494.31 Measured High confidence 4129.6 1.18181
    ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] C15orf15 30651.3 Squared 38253.3 1.24802
    vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] TCIRG1 8636.95 Measured Low confidence 9122.21 1.05618
    336 60s ribosomal protein l11. [swissprot;acc:p39026] RPL11 50.3167 Rooted High confidence 45.4063 1.10814
    cgi-121 protein; prpk (p53-related protein kinase)-binding protein. [refseq;acc:nm_016058] TPRKB 9142.34 Measured Low confidence 9654.91 1.05607
    cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] CDK2AP1 312 Ranked High confidence 284 1.09859
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] POLE4 3751.3 Measured 4431.34 1.18128
    j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] RBPJ 46785.7 Squared 58383.2 1.24789
    max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 67.7178 Rooted Low confidence 71.2386 1.05199
    nude nuclear distribution gene e homolog like 1 (a. nidulans); lis1-interacting protein nudel; endooligopeptidase a. [refseq;acc:nm_030808] NDEL1 48969.6 Squared 45455.3 1.07731
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 202.616 Ranked 194.878 1.03971
    337 60s ribosomal protein l12. [swissprot;acc:p30050] no value 243.583 High confidence 267.527 1.0983
    carboxypeptidase b precursor. [refseq;acc:nm_020361] CPA6 77.5801 Rooted 70.0182 1.108
    homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value 20446.1 Measured 24136.4 1.18049
    human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] HIVEP3 46785.7 Squared 58383.2 1.24789
    max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 67.723 Rooted Low confidence 71.2422 1.05196
    mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] GTPBP3 9204.48 Measured 9720.58 1.05607
    rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] C19orf2 49748.9 Squared 46179.8 1.07729
    serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] CDKL1 201.873 Ranked 194.181 1.03961
    338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] no value 243.583 High confidence 267.528 1.0983
    homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 20446.1 Measured 24136.4 1.18049
    mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] CPA3 77.58 Rooted 70.0181 1.108
    max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 67.7254 Low confidence 71.2438 1.05195

    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/