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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 880 to 929 of 6456 in total
    Value Type	Ranked
    Interaction Map High confidence
    Filtered 1
    Rank Hugo description Network Comparison Type red green network_comparison 440 NDC80 highly expressed in cancer, rich in leucine heptad repeats. [source:refseq;acc:nm_006101] Divided 231.802 249.983 1.07843 441 GRAP grb2-related adaptor protein. [source:swissprot;acc:q13588] Divided 223.457 207.222 1.07835 441 TIMM22 mitochondrial import inner membrane translocase subunit tim22. [source:swissprot;acc:q9y584] Subtracted 210.225 226.578 16.353 442 ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140] Divided 223.802 207.55 1.0783 442 ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [source:refseq;acc:nm_145691] Subtracted 210.225 226.578 16.353 443 NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117] Divided 223.79 207.539 1.0783 443 UQCRB ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [source:swissprot;acc:p14927] Subtracted 210.225 226.578 16.353 444 NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443] Divided 223.801 207.549 1.0783 444 NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087] Subtracted 250.053 233.725 16.328 445 GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366] Subtracted 250.858 234.563 16.295 445 NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903] Divided 223.801 207.549 1.0783 446 GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [source:swissprot;acc:p29354] Divided 224.049 207.785 1.07827 446 GRB2 growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [source:swissprot;acc:p29354] Subtracted 224.049 207.785 16.264 447 NEK2 serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [source:swissprot;acc:p51955] Divided 224.049 207.785 1.07827 447 NEK2 serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [source:swissprot;acc:p51955] Subtracted 224.049 207.785 16.264 448 ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140] Subtracted 223.802 207.55 16.252 448 MACF1 microtubule-actin crosslinking factor 1, isoform 4. [source:swissprot;acc:q96pk2] Divided 228.468 246.338 1.07822 449 DST bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [source:swissprot;acc:q03001] Divided 228.463 246.33 1.07821 449 NAV1 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443] Subtracted 223.801 207.549 16.252 450 NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903] Subtracted 223.801 207.549 16.252 450 SRP9 signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458] Divided 235.94 218.837 1.07815 451 NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117] Subtracted 223.79 207.539 16.251 451 POLR3C polymerase (rna) iii (dna directed) (62kd). [source:refseq;acc:nm_006468] Divided 239.092 257.705 1.07785 452 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36] Divided 224.161 207.972 1.07784 452 POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195] Subtracted 221.522 205.286 16.236 453 PXN paxillin. [source:swissprot;acc:p49023] Subtracted 221.522 205.286 16.236 453 SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661] Divided 224.161 207.972 1.07784 454 40s ribosomal protein s26. [source:swissprot;acc:p02383] Divided 210.224 226.578 1.07779 454 GRAP grb2-related adaptor protein. [source:swissprot;acc:q13588] Subtracted 223.457 207.222 16.235 455 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36] Subtracted 224.161 207.972 16.189 455 TIMM22 mitochondrial import inner membrane translocase subunit tim22. [source:swissprot;acc:q9y584] Divided 210.225 226.578 1.07779 456 ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [source:refseq;acc:nm_145691] Divided 210.225 226.578 1.07779 456 SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661] Subtracted 224.161 207.972 16.189 457 FNBP1 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [source:sptrembl;acc:q96lh6] Subtracted 210.578 226.764 16.186 457 UQCRB ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [source:swissprot;acc:p14927] Divided 210.225 226.578 1.07779 458 DDX18 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1] Subtracted 251.653 235.506 16.147 458 SRP9 signal recognition particle 9 kda protein (srp9). [source:swissprot;acc:p49458] Divided 235.922 218.925 1.07764 459 BAG3 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [source:swissprot;acc:o95817] Divided 233.529 216.737 1.07748 459 RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182] Subtracted 250.538 234.401 16.137 460 RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424] Subtracted 186.52 170.42 16.1 460 SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428] Divided 223.648 207.62 1.0772 461 ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464] Subtracted 186.52 170.42 16.1 461 KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887] Divided 223.648 207.62 1.0772 462 MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [source:refseq;acc:nm_032390] Divided 254.434 236.224 1.07709 462 POLR2H dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [source:swissprot;acc:p52434] Subtracted 236.662 252.708 16.046 463 POLR3F dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [source:swissprot;acc:q9h1d9] Divided 238.921 257.327 1.07704 463 SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428] Subtracted 223.648 207.62 16.028 464 FNBP1 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [source:sptrembl;acc:q96lh6] Divided 210.578 226.764 1.07686 464 KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [source:swissprot;acc:q13887] Subtracted 223.648 207.62 16.028 465 CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544] Divided 248.152 267.226 1.07686 Legend: - Rank is the rank after comparing the two networks - 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/