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 description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1344 to 1393 of 6456 in total
    Value Type  : Ranked
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Network Comparison Type
    		red
    		green
    		network_comparison
    672 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 Divided 210.739 199.398 1.05688
    673 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] DOK2 Subtracted 216.504 204.622 11.882
    peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] CASK Divided 226.497 214.355 1.05664
    674 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] DOK1 Subtracted 216.504 204.622 11.882
    hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] HIF3A Divided 226.497 214.355 1.05664
    675 single-minded homolog 1. [swissprot;acc:p81133] SIM1
    tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] FRK Subtracted 216.504 204.622 11.882
    676 dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] POLR2G Divided 232.469 245.613 1.05654
    ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] MRTO4 Subtracted 245.84 257.636 11.796
    677 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] FBL 245.246 233.483 11.763
    u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] LSM4 Divided 228.944 216.745 1.05628
    678 peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] PPIL4 Subtracted 226.135 214.405 11.73
    sorting nexin 5. [swissprot;acc:q9y5x3] SNX5 Divided 208.482 220.175 1.05609
    679 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] no value 132.413 125.389 1.05602
    sorting nexin 5. [swissprot;acc:q9y5x3] SNX5 Subtracted 208.482 220.175 11.693
    680 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Divided 132.413 125.389 1.05602
    sr rich protein. [refseq;acc:nm_032870] SFRS18 Subtracted 225.293 213.64 11.653
    681 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Divided 132.413 125.389 1.05602
    nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] SNW1 Subtracted 220.593 208.987 11.606
    682 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Divided 132.413 125.389 1.05602
    upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] NAT10 Subtracted 246.055 234.458 11.597
    683 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Divided 132.413 125.389 1.05602
    osteoclast stimulating factor 1. [swissprot;acc:q92882] OSTF1 Subtracted 231.809 243.289 11.48
    684 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Divided 132.413 125.389 1.05602
    phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] PFAS Subtracted 223.58 235.027 11.447
    685 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] ATIC
    homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Divided 132.413 125.389 1.05602
    686 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value
    multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] PAICS Subtracted 223.58 235.027 11.447
    687 dendritic cell protein. [refseq;acc:nm_006360] EIF3M 223.121 211.685 11.436
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Divided 132.413 125.389 1.05602
    688 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] POLR2D 237.554 250.823 1.05586
    potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] CPXM2 Subtracted 223.121 211.685 11.436
    689 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] CPN1
    t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] TCP1 Divided 135.379 128.225 1.05579
    690 cpz gene product. [refseq;acc:nm_003652] CPZ Subtracted 223.121 211.685 11.436
    nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] SNW1 Divided 220.593 208.987 1.05553
    691 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] BCAS2 217.602 206.195 1.05532
    carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] CPE Subtracted 223.121 211.685 11.436
    692 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] CDC5L Divided 217.602 206.195 1.05532
    potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] CPXM1 Subtracted 223.121 211.685 11.436
    693 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] BCAS2 217.602 206.195 11.407
    rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] NOVA1 Divided 222.554 234.847 1.05524
    694 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] CDC5L Subtracted 217.602 206.195 11.407
    dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] POLE Divided 241.907 229.35 1.05475
    695 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 Subtracted 210.739 199.398 11.341
    peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] PPIL4 Divided 226.135 214.405 1.05471
    696 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 Subtracted 210.739 199.398 11.341
    sr rich protein. [refseq;acc:nm_032870] SFRS18 Divided 225.293 213.64 1.05455
    697 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] FTH1 220.444 209.113 1.05419

    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/