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 Value Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2251 to 2300 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    282 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] NOX5 Measured Low confidence 7904.14 8377.35 1.05987
    rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] RAP1GAP High confidence 3119.98 2579.49 1.20953
    splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] SF3A2 Rooted 57.9819 64.9302 1.11984
    spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] SPSB1 Low confidence 65.1829 68.7965 1.05544
    stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] CLEC11A Squared High confidence 59704 76460.4 1.28066
    swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] SMARCD1 Low confidence 49771.1 45810.4 1.08646
    283 60s ribosomal protein l11. [swissprot;acc:p39026] RPL11 Ranked High confidence 241.828 267.346 1.10552
    ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] NFYA Rooted Low confidence 67.8224 71.5783 1.05538
    deltex 2. [refseq;acc:nm_020892] DTX2 Squared High confidence 6627.24 8484.19 1.2802
    hepatocellular carcinoma-associated antigen 127. [refseq;acc:nm_018684] KIAA1166 Low confidence 48000.9 44200.7 1.08598
    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). [swissprot;acc:q13887] KLF5 Rooted High confidence 57.9819 64.9302 1.11984
    nadph oxidase 4. [refseq;acc:nm_016931] NOX4 Measured Low confidence 7904.2 8377.39 1.05987
    polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] POLI High confidence 5221.28 6314.35 1.20935
    upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] UBP1 Ranked Low confidence 219.722 210.484 1.04389
    284 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] CLEC3A Squared High confidence 59464 76120.8 1.28012
    crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] BCAR1 Ranked 224.657 203.235 1.10541
    cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] CSRP1 Rooted 51.8647 46.3161 1.1198
    kinesin-like protein kif3c. [swissprot;acc:o14782] KIF3C Squared Low confidence 47603.5 43837.2 1.08592
    nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] NOX3 Measured 7904.17 8377.37 1.05987
    paxillin. [swissprot;acc:p49023] PXN High confidence 5221.28 6314.35 1.20935
    potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] KCND2 Rooted Low confidence 61.1842 57.9792 1.05528
    tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [swissprot;acc:q9h2k2] TNKS2 Ranked 214.675 205.692 1.04367
    285 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] DDX54 Rooted High confidence 48.4278 54.2262 1.11973
    deltex homolog 1; hdx-1. [refseq;acc:nm_004416] DTX1 Squared 6680.89 8549.44 1.27969
    kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] KIF3B Low confidence 47581.4 43844.3 1.08524
    nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] NOX1 Measured 7904.2 8377.39 1.05987
    poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] PAPOLA High confidence 23326.5 19296.4 1.20885
    source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] STT3B Rooted Low confidence 70.6427 74.545 1.05524
    t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] CCT4 Ranked High confidence 224.647 203.242 1.10532
    transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] TAF4 Low confidence 202.354 211.175 1.04359
    286 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] CSNK1A1 Squared 51001.6 47002.7 1.08508
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] ATG4A Rooted 100.524 95.2715 1.05513
    enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] NEDD9 Ranked High confidence 224.633 203.251 1.1052
    exocyst complex component sec5. [swissprot;acc:q96kp1] EXOC2 Measured 23316 19288.8 1.20878
    sedlin. [swissprot;acc:o14582] ZNF547 Low confidence 9059.8 9601.05 1.05974
    smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] CSRP2 Rooted High confidence 51.8717 46.3287 1.11965
    t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] PBK Squared 6693.64 8564.94 1.27956
    transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] TAF4B Ranked Low confidence 202.356 211.174 1.04358
    287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] RPS4Y2 High confidence 240.758 266.079 1.10517
    adiponectin receptor 2. [refseq;acc:nm_024551] ADIPOR2 Measured Low confidence 7170.39 7598.55 1.05971
    kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] KHDRBS3 Squared High confidence 6693.64 8564.94 1.27956
    likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] SHCBP1 Rooted 51.8714 46.3281 1.11965
    nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] NFYC Low confidence 68.4997 72.2554 1.05483
    poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] PAPOLG Measured High confidence 23303.1 19279.5 1.2087
    rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] GIPC1 Ranked Low confidence 210.132 201.397 1.04337
    swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078] SMARCD3 Squared 49638.8 45746.6 1.08508
    288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] no value Ranked High confidence 240.758 266.078 1.10517
    blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526] BET1L Measured Low confidence 8155.32 8641.69 1.05964
    casein kinase i alpha s-like. [refseq;acc:nm_145203] CSNK1A1L Squared 51000.2 47002.1 1.08506
    cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] NUDT21 Rooted 69.4692 73.2638 1.05462

    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/