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 [...,...].
    Network Comparison Type Rank Gene Value Type description Interaction Map Hugo network_comparison Filtered red green
    Results: HTML CSV LaTeX Showing element 2651 to 2700 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Value Type
    		description
    		Interaction Map
    		Hugo
    		network_comparison
    		red
    		green
    332 Ranked dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Low confidence DYNC1I1 1.03981 209.495 201.474
    neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence NEUROD6 1.09859 312 284
    Squared nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 1.25432 14464.3 18142.8
    zinc finger protein, subfamily 1a, 5; zinc finger transcription factor pegasus. [refseq;acc:nm_022466] Low confidence IKZF5 1.07853 50786.2 47088.3
    Rooted l-lactate dehydrogenase c chain (ec 1.1.1.27) (ldh-c) (ldh testis subunit) (ldh-x). [swissprot;acc:p07864] LDHC 1.052 67.7165 71.2378
    shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] High confidence SHROOM3 1.10894 60.6732 67.2827
    333 Measured nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] PRPF19 1.18299 5039.63 5961.83
    vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Low confidence ATP6V0A2 1.05634 8639.75 9126.51
    Ranked neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] High confidence NEUROD1 1.09859 312 284
    protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42] Low confidence C20orf43 1.03972 200.482 208.446
    Squared nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] High confidence NUBP2 1.25432 14464.3 18142.8
    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] Low confidence PAFAH1B1 1.07853 50786.2 47088.3
    Rooted l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [swissprot;acc:p00338] LDHA 1.052 67.7165 71.2378
    nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] High confidence GTPBP4 1.10857 49.0526 54.3781
    334 Measured sec14-like protein 1. [swissprot;acc:q92503] Low confidence SEC14L1 1.05633 9271.66 9793.93
    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] High confidence SEPT4 1.18298 14924.4 17655.2
    Ranked coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250] Low confidence BICD2 1.03971 202.616 194.878
    neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence NEUROD4 1.09859 312 284
    Squared ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] CANT1 1.24894 64975.9 81151.2
    nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] Low confidence no value 1.07836 49618.3 46012.8
    Rooted l-lactate dehydrogenase b chain (ec 1.1.1.27) (ldh-b) (ldh heart subunit) (ldh-h). [swissprot;acc:p07195] LDHB 1.052 67.7167 71.2379
    pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] High confidence PLRG1 1.10844 58.6096 64.9655
    335 Measured probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] DDX56 1.18181 3494.31 4129.6
    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] Low confidence TCIRG1 1.05618 8636.95 9122.21
    Ranked bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] BICD1 1.03971 202.616 194.878
    chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] High confidence CHD5 1.09859 312 284
    Squared nude nuclear distribution gene e homolog 1 (a. nidulans); lis1-interacting protein nude1, rat homolog. [refseq;acc:nm_017668] Low confidence NDE1 1.07759 48994 45466.4
    ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] High confidence C15orf15 1.24802 30651.3 38253.3
    Rooted 40s ribosomal protein s11. [swissprot;acc:p04643] RPS11 1.10841 50.4705 45.5342
    clip-associating protein 1; drosophila 'multiple asters' (mast)-like homolog 1. [refseq;acc:nm_015282] Low confidence CLASP1 1.052 67.7167 71.2379
    336 Measured cgi-121 protein; prpk (p53-related protein kinase)-binding protein. [refseq;acc:nm_016058] TPRKB 1.05607 9142.34 9654.91
    dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] High confidence POLE4 1.18128 3751.3 4431.34
    Ranked 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 1.09859 312 284
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Low confidence TFIP11 1.03971 202.616 194.878
    Squared j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] High confidence RBPJ 1.24789 46785.7 58383.2
    nude nuclear distribution gene e homolog like 1 (a. nidulans); lis1-interacting protein nudel; endooligopeptidase a. [refseq;acc:nm_030808] Low confidence NDEL1 1.07731 48969.6 45455.3
    Rooted 60s ribosomal protein l11. [swissprot;acc:p39026] High confidence RPL11 1.10814 50.3167 45.4063
    max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Low confidence MXI1 1.05199 67.7178 71.2386
    337 Measured homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence no value 1.18049 20446.1 24136.4
    mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Low confidence GTPBP3 1.05607 9204.48 9720.58
    Ranked 60s ribosomal protein l12. [swissprot;acc:p30050] High confidence no value 1.0983 243.583 267.527
    serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] Low confidence CDKL1 1.03961 201.873 194.181
    Squared human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] High confidence HIVEP3 1.24789 46785.7 58383.2
    rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Low confidence C19orf2 1.07729 49748.9 46179.8
    Rooted carboxypeptidase b precursor. [refseq;acc:nm_020361] High confidence CPA6 1.108 77.5801 70.0182
    max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Low confidence MXD4 1.05196 67.723 71.2422
    338 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] High confidence HOXB4 1.18049 20446.1 24136.4
    ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Low confidence UBE2I 1.05583 9229.69 9745
    Ranked 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] High confidence no value 1.0983 243.583 267.528
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Low confidence TXNL4A 1.03958 202.572 194.86

    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/