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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1108 to 1157 of 12912 in total
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		red
    		green
    		network_comparison
    277 SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Squared 16120.1 20665.7 1.28198
    278 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
    ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Rooted 65.9938 73.9449 1.12048
    LBX1 transcription factor lbx1. [swissprot;acc:p52954] Measured 3119.98 2579.49 1.20953
    RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] Ranked 241.399 267.088 1.10642
    279 GPSM2 mosaic protein lgn. [swissprot;acc:p81274] Measured 3119.98 2579.49 1.20953
    MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Squared 15569.5 19953.6 1.28158
    RBBP7 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Ranked 252.644 228.42 1.10605
    WASL neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Rooted 66.0989 74.0609 1.12046
    280 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 57.9068 64.8562 1.12001
    MSI1 musashi 1. [refseq;acc:nm_002442] Squared 15569.5 19953.6 1.28158
    MTA1 metastasis-associated protein mta1. [swissprot;acc:q13330] Ranked 252.512 228.356 1.10578
    RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Measured 3119.98 2579.49 1.20953
    281 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Ranked 241.808 267.335 1.10557
    GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Measured 3119.98 2579.49 1.20953
    SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Rooted 57.9068 64.8562 1.12001
    ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Squared 15569.5 19953.6 1.28158
    282 CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 59704 76460.4 1.28066
    RAP1GAP rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Measured 3119.98 2579.49 1.20953
    RBBP4 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Ranked 252.39 228.297 1.10553
    SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Rooted 57.9819 64.9302 1.11984
    283 DTX2 deltex 2. [refseq;acc:nm_020892] Squared 6627.24 8484.19 1.2802
    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). [swissprot;acc:q13887] Rooted 57.9819 64.9302 1.11984
    POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Measured 5221.28 6314.35 1.20935
    RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Ranked 241.828 267.346 1.10552
    284 BCAR1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 224.657 203.235 1.10541
    CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Squared 59464 76120.8 1.28012
    CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Rooted 51.8647 46.3161 1.1198
    PXN paxillin. [swissprot;acc:p49023] Measured 5221.28 6314.35 1.20935
    285 CCT4 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Ranked 224.647 203.242 1.10532
    DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Rooted 48.4278 54.2262 1.11973
    DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Squared 6680.89 8549.44 1.27969
    PAPOLA poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 23326.5 19296.4 1.20885
    286 CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Rooted 51.8717 46.3287 1.11965
    EXOC2 exocyst complex component sec5. [swissprot;acc:q96kp1] Measured 23316 19288.8 1.20878
    NEDD9 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] Ranked 224.633 203.251 1.1052
    PBK 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] Squared 6693.64 8564.94 1.27956
    287 KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]
    PAPOLG poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 23303.1 19279.5 1.2087
    RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Ranked 240.758 266.079 1.10517
    SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Rooted 51.8714 46.3281 1.11965
    288 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Ranked 240.758 266.078 1.10517
    CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Measured 23422.4 19380.3 1.20857
    CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Rooted 51.8789 46.3416 1.11949
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Squared 6693.64 8564.94 1.27956
    289 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Ranked 272.781 246.892 1.10486
    KHDRBS2 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Squared 6693.64 8564.94 1.27956
    LSM6 u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Measured 4682.88 5646.19 1.20571
    PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Rooted 57.4274 64.2609 1.11899
    290 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 75.6323 67.6572 1.11788

    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/