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 red Interaction Map Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 2308 to 2357 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		red
    		Interaction Map
    		green
    		network_comparison
    289 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] KHDRBS2 Squared 6693.64 High confidence 8564.94 1.27956
    myelin p2 protein. [swissprot;acc:p02689] PMP2 49695.7 Low confidence 45815.4 1.08469
    pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] PRPF31 Rooted 57.4274 High confidence 64.2609 1.11899
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Measured 7752.95 Low confidence 8214.32 1.05951
    u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] LSM6 4682.88 High confidence 5646.19 1.20571
    290 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Squared 15734.4 20126.8 1.27916
    atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value Rooted 75.6323 67.6572 1.11788
    fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] FABP4 Squared 49694.4 Low confidence 45814.8 1.08468
    lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] LAPTM4B Ranked 210 201.325 1.04309
    rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414] RAB3GAP2 Rooted 69.4692 73.2638 1.05462
    ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] RRM2 Ranked 231.969 High confidence 210.064 1.10428
    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] E2F1 Measured 6885.52 Low confidence 7293.37 1.05923
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] TFIP11 4991.48 High confidence 6014.08 1.20487
    291 neuronal guanine nucleotide exchange factor. [refseq;acc:nm_019850] NGEF Squared 48964.5 Low confidence 45143 1.08465
    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] NFYB Ranked 251.679 High confidence 228.037 1.10368
    pl6 protein (placental protein 6). [swissprot;acc:q12893] TMEM115 209.995 Low confidence 201.322 1.04308
    putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] UBAC1 Measured 44490.5 High confidence 36927.5 1.20481
    splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] SF3A3 Rooted 71.0039 Low confidence 74.8814 1.05461
    tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] CLEC3B Squared 59016.1 High confidence 75486.9 1.27909
    transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] E2F2 Measured 6885.52 Low confidence 7293.37 1.05923
    ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] no value Rooted 113.983 High confidence 101.979 1.11771
    292 40s ribosomal protein s15a. [swissprot;acc:p39027] RPS15A Ranked 241.411 266.414 1.10357
    60s ribosomal protein l27. [swissprot;acc:p08526] RPL27 Measured 7860.4 Low confidence 8325.71 1.0592
    lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] LAPTM4A Ranked 209.995 201.322 1.04308
    neuralized-like. [refseq;acc:nm_004210] NEURL Squared 6828.26 High confidence 8728.66 1.27831
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 Measured 4641.09 5588.75 1.20419
    phosphoserine aminotransferase (ec 2.6.1.52) (psat). [swissprot;acc:q9y617] PSAT1 Squared 56826.7 Low confidence 61634.7 1.08461
    splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] SF3A1 Rooted 71.0039 74.8814 1.05461
    u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] LSM6 56.48 High confidence 63.119 1.11755
    293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] no value Ranked 240.782 265.717 1.10356
    kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] KYNU Squared 35991.8 46002.9 1.27815
    mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] SMAD3 49043.9 Low confidence 45220 1.08456
    nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 Measured 4641.09 High confidence 5588.75 1.20419
    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] KCND3 Rooted 61.2714 Low confidence 58.111 1.05439
    probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] ATP2C2 Ranked 218.785 209.763 1.04301
    short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] TRPC4 Rooted 63.0715 High confidence 56.4506 1.11729
    splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] SF3B2 Measured 7675.19 Low confidence 8129.16 1.05915
    294 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] AGPAT2 Squared 30826.5 High confidence 39383.9 1.2776
    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] BCCIP Ranked 240.782 265.717 1.10356
    cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] CSTF3 Measured 22515.5 18702.6 1.20387
    fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] FABP3 Squared 49635.2 Low confidence 45787.9 1.08402
    jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] JAG2 Ranked 218.715 209.71 1.04294
    nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 Rooted 70.1377 73.9413 1.05423
    segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] DVL1 59.0296 High confidence 65.951 1.11725
    ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462] UBE2G1 Measured 7590.39 Low confidence 8039.23 1.05913
    295 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] no value Squared 30807.7 High confidence 39351.7 1.27733
    5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [swissprot;acc:q99707] MTR Measured 9113.16 Low confidence 9650.42 1.05895
    multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] SCYE1 Ranked 223.273 High confidence 202.423 1.103
    myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] MEF2D 218.713 Low confidence 209.709 1.04294
    ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] RGL1 Measured 13261.9 High confidence 11017.8 1.20368

    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/