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 Network Comparison Type Hugo Value Type description Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 2301 to 2350 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    288 CSRP3 Rooted lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] High confidence 1.11949 51.8789 46.3416
    KHDRBS1 Squared kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1.27956 6693.64 8564.94
    NUDT21 Rooted 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] Low confidence 1.05462 69.4692 73.2638
    SNRPD1 Ranked small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 1.04314 200.288 192.004
    289 no value hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] High confidence 1.10486 272.781 246.892
    ITGB1BP2 Rooted integrin beta-1 binding protein 2 (melusin) (mstp015). [swissprot;acc:q9ukp3] Low confidence 1.05462 69.4692 73.2638
    KHDRBS2 Ranked kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 1.04311 209.31 200.66
    Squared High confidence 1.27956 6693.64 8564.94
    LSM6 Measured u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] 1.20571 4682.88 5646.19
    PMP2 Squared myelin p2 protein. [swissprot;acc:p02689] Low confidence 1.08469 49695.7 45815.4
    PRPF31 Rooted pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] High confidence 1.11899 57.4274 64.2609
    SF3B1 Measured splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Low confidence 1.05951 7752.95 8214.32
    290 no value Rooted atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] High confidence 1.11788 75.6323 67.6572
    E2F1 Measured transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Low confidence 1.05923 6885.52 7293.37
    FABP4 Squared fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] 1.08468 49694.4 45814.8
    LAPTM4B Ranked lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] 1.04309 210 201.325
    NCBP2 Squared 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] High confidence 1.27916 15734.4 20126.8
    RAB3GAP2 Rooted rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414] Low confidence 1.05462 69.4692 73.2638
    RRM2 Ranked ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] High confidence 1.10428 231.969 210.064
    TFIP11 Measured tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 1.20487 4991.48 6014.08
    291 no value Rooted ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 1.11771 113.983 101.979
    CLEC3B Squared tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 1.27909 59016.1 75486.9
    E2F2 Measured transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Low confidence 1.05923 6885.52 7293.37
    NFYB Ranked nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] High confidence 1.10368 251.679 228.037
    NGEF Squared neuronal guanine nucleotide exchange factor. [refseq;acc:nm_019850] Low confidence 1.08465 48964.5 45143
    SF3A3 Rooted splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] 1.05461 71.0039 74.8814
    TMEM115 Ranked pl6 protein (placental protein 6). [swissprot;acc:q12893] 1.04308 209.995 201.322
    UBAC1 Measured putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 1.20481 44490.5 36927.5
    292 LAPTM4A Ranked lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] Low confidence 1.04308 209.995 201.322
    LSM6 Rooted u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] High confidence 1.11755 56.48 63.119
    NEURL Squared neuralized-like. [refseq;acc:nm_004210] 1.27831 6828.26 8728.66
    NUBP1 Measured nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 1.20419 4641.09 5588.75
    PSAT1 Squared phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] Low confidence 1.08461 56826.7 61634.7
    RPL27 Measured 60s ribosomal protein l27. [swissprot;acc:p08526] 1.0592 7860.4 8325.71
    RPS15A Ranked 40s ribosomal protein s15a. [swissprot;acc:p39027] High confidence 1.10357 241.411 266.414
    SF3A1 Rooted splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Low confidence 1.05461 71.0039 74.8814
    293 no value Ranked 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] High confidence 1.10356 240.782 265.717
    ATP2C2 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Low confidence 1.04301 218.785 209.763
    KCND3 Rooted potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] 1.05439 61.2714 58.111
    KYNU Squared kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] High confidence 1.27815 35991.8 46002.9
    NUBP2 Measured nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 1.20419 4641.09 5588.75
    SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Low confidence 1.05915 7675.19 8129.16
    SMAD3 Squared mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] 1.08456 49043.9 45220
    TRPC4 Rooted short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] High confidence 1.11729 63.0715 56.4506
    294 AGPAT2 Squared 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 1.2776 30826.5 39383.9
    BCCIP Ranked brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 1.10356 240.782 265.717
    CSTF3 Measured cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 1.20387 22515.5 18702.6
    DVL1 Rooted segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 1.11725 59.0296 65.951
    FABP3 Squared fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Low confidence 1.08402 49635.2 45787.9
    JAG2 Ranked jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] 1.04294 218.715 209.71

    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/