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 description Value Type Hugo Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 2380 to 2429 of 66312 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Value Type
    		Hugo
    		Interaction Map
    		network_comparison
    		red
    		green
    298 myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Ranked MEF2A Low confidence 1.04294 218.715 209.71
    n-acetylglutamate synthase. [refseq;acc:nm_153006] Squared NAGS 1.08332 55642.1 60278.3
    ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] no value High confidence 1.27336 14247.4 18142.1
    squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Rooted SART1 1.11683 57.6823 64.4212
    u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Measured no value 1.20262 4633.92 5572.85
    299 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN Low confidence 1.05855 8904.93 9426.29
    ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] no value High confidence 1.20203 4914.27 5907.12
    calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Ranked CAPN1 1.10281 268.635 243.592
    endoribonuclease dicer (ec 3.1.26.-) (helicase with rnase motif) (helicase-moi). [swissprot;acc:q9upy3] DICER1 Low confidence 1.0429 208.915 200.322
    grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Squared GRPEL1 1.0833 51585.2 47618.4
    heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [swissprot;acc:q16082] Rooted HSPB2 1.05366 68.172 71.8299
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Squared CRK High confidence 1.27238 28896.2 36767
    segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted DVL3 1.11638 59.026 65.8955
    300 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Ranked ATP2C1 Low confidence 1.04289 218.661 209.669
    metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] PITRM1 High confidence 1.10196 150.959 166.351
    mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Rooted MKI67IP 1.11586 48.1584 53.7378
    nitrogen fixation cluster-like. [refseq;acc:nm_014301] Measured ISCU Low confidence 1.0584 8667.67 9173.88
    plasma membrane calcium-transporting atpase 3 (ec 3.6.3.8) (pmca3) (plasma membrane calcium pump isoform 3) (plasma membrane calcium atpase isoform 3). [swissprot;acc:q16720] Squared ATP2B3 1.08309 49511.1 45712.9
    secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Rooted no value 1.05347 70.2592 74.0161
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Squared ABL2 High confidence 1.27238 28896.2 36767
    u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Measured SNRPA1 1.20203 4914.27 5907.12
    301 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Ranked ALG1 1.10193 150.982 166.372
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Measured no value 1.20078 13768.2 11466
    epsin 3. [refseq;acc:nm_017957] EPN3 Low confidence 1.05832 8559.94 9059.13
    integrin alpha-5 precursor (fibronectin receptor alpha subunit) (integrin alpha-f) (vla-5) (cd49e). [swissprot;acc:p08648] Squared ITGA5 1.08274 57397.4 53011.1
    large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Ranked SLC7A8 1.04287 205.154 196.72
    mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Rooted no value High confidence 1.11517 203.673 182.638
    prefoldin subunit 1. [swissprot;acc:o60925] PFDN1 Low confidence 1.05347 70.2592 74.0161
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Squared no value High confidence 1.27238 28896.2 36767
    302 60s ribosomal protein l26. [swissprot;acc:q02877] Ranked RPL26 1.10185 242.326 267.008
    cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted PSCD1 1.11517 203.673 182.638
    integrin alpha-v precursor (vitronectin receptor alpha subunit) (cd51 antigen). [swissprot;acc:p06756] Squared ITGAV Low confidence 1.08274 57397.4 53011.1
    pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Measured PLDN High confidence 1.19999 5894.75 7073.65
    secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] Rooted SMOC2 Low confidence 1.05347 70.2592 74.0161
    tfiih basal transcription factor complex p34 subunit (basic transcription factor 2 34 kda subunit) (btf2-p34) (general transcription factor iih polypeptide 3). [swissprot;acc:q13889] Measured GTF2H3 1.05818 9243.98 9781.77
    tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Squared HCK High confidence 1.27238 28896.2 36767
    xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Ranked XPR1 Low confidence 1.04274 209.12 200.548
    303 60s ribosomal protein l35. [swissprot;acc:p42766] RPL35 High confidence 1.10179 242.333 266.999
    choline dehydrogenase. [refseq;acc:nm_018397] Rooted CHDH Low confidence 1.05347 70.2592 74.0161
    crk-like protein. [swissprot;acc:p46109] Squared CRKL High confidence 1.27238 28896.2 36767
    cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted PSCD2 1.11517 203.673 182.638
    homeobox protein nkx-6.1. [swissprot;acc:p78426] Measured NKX6-1 Low confidence 1.05813 9810.95 10381.3
    homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked HOMER3 1.04273 210.057 201.45
    integrin alpha-8. [swissprot;acc:p53708] Squared ITGA8 1.08274 57397.4 53011.1
    serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Measured PPP1CC High confidence 1.1998 22268.8 18560.4
    304 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Ranked no value 1.1017 242.339 266.986
    cytohesin 4. [swissprot;acc:q9uia0] Rooted PSCD4 1.11517 203.673 182.638
    integrin alpha-iib precursor (platelet membrane glycoprotein iib) (gpalpha iib) (gpiib) (cd41 antigen). [swissprot;acc:p08514] Squared ITGA2B Low confidence 1.08274 57397.4 53011.1
    kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked KHDRBS1 1.04271 209.232 200.662
    nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [refseq;acc:nm_177400] Measured NKX6-2 1.05813 9810.95 10381.3

    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/