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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 1758 to 1807 of 66312 in total
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		network_comparison
    		green
    110 PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Measured Divided High confidence 4366.44 1.35116 5899.76
    SASH1 sam and sh3 domain containing 1. [refseq;acc:nm_015278] Squared Subtracted Low confidence 55150.6 8510.7 46639.9
    VPS18 vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Rooted 69.2771 5.9537 75.2308
    111 ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Squared High confidence 79779.8 28304.2 108084
    BRP44 brain protein 44. [swissprot;acc:o95563] Measured Low confidence 10392.1 867.6 11259.7
    CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Rooted Divided High confidence 49.2923 1.26585 62.3969
    CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Measured Subtracted 12365.2 2459.7 14824.9
    DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Rooted Low confidence 55.8923 5.9093 61.8016
    DLGAP1 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Ranked 197.779 14.204 211.983
    DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Divided High confidence 332.925 1.24563 267.274
    GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Subtracted 209.299 39.888 249.187
    HAAO 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Squared Divided Low confidence 65044.3 1.15248 74962.3
    JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Rooted Subtracted High confidence 33.9632 15.5377 18.4255
    MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Measured Divided Low confidence 11285.3 1.0937 10318.5
    MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Squared High confidence 19321 1.54043 12542.6
    NEURL neuralized-like. [refseq;acc:nm_004210] Rooted Low confidence 61.317 1.08191 66.3394
    PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Measured High confidence 4366.44 1.35116 5899.76
    STXBP1 syntaxin binding protein 1 (unc-18 homolog) (unc-18a) (unc-18-1) (n- sec1) (rbsec1) (p67). [swissprot;acc:q64320] Squared Subtracted Low confidence 74200.8 8503.9 65696.9
    VPS33A vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Ranked Divided 203.914 1.07217 190.189
    112 no value intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Squared 59879.6 1.15208 51975.3
    AGL glycogen debranching enzyme (glycogen debrancher) [includes: 4-alpha- glucanotransferase (ec 2.4.1.25) (oligo-1,4-1,4-glucantransferase); amylo-alpha-1,6-glucosidase (ec 3.2.1.33) (amylo-1,6-glucosidase) (dextrin 6-alpha-d-glucosidase)]. [swissprot;acc:p35573] Subtracted 61349.6 8501.2 52848.4
    ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Measured High confidence 11757.8 2405.69 9352.11
    CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Rooted Divided 49.3267 1.26537 62.4167
    CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Ranked Low confidence 197.762 1.07206 212.013
    CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] Squared Subtracted High confidence 96730.5 27443.8 69286.7
    DLGAP4 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Ranked Low confidence 197.779 14.204 211.983
    LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Rooted Divided 71.084 1.08102 76.8432
    MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Measured 11285.3 1.0937 10318.5
    MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Squared High confidence 19321 1.54043 12542.6
    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] Ranked 332.874 1.24557 267.246
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Subtracted 275.754 39.846 235.908
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Rooted Low confidence 55.9786 5.8855 61.8641
    SLC16A5 monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] Measured 10351.8 859 11210.8
    SMPD2 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Rooted High confidence 33.9632 15.5377 18.4255
    SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Measured Divided 4366.44 1.35116 5899.76
    113 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Low confidence 11285.3 1.0937 10318.5
    ARRB2 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Rooted High confidence 80.4705 1.26165 101.526
    ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] Measured Subtracted 4800.81 2331.9 7132.71
    BRP44 brain protein 44. [swissprot;acc:o95563] Squared Low confidence 62640.6 8397.7 71038.3
    CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Ranked Divided 197.763 1.07205 212.011
    CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Squared Subtracted High confidence 96602.7 27391.5 69211.2
    KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked Divided 332.874 1.24557 267.246
    MAN1B1 endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (ec 3.2.1.113) (er alpha-1,2-mannosidase) (mannosidase alpha class 1b member 1) (man9glcnac2-specific processing alpha-mannosidase). [swissprot;acc:q9ukm7] Rooted Low confidence 66.9562 1.08017 72.3243
    MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared High confidence 19321 1.54043 12542.6
    PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Ranked Subtracted 194.372 39.832 234.204
    SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Squared Divided Low confidence 59884.7 1.14972 68850.8
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Ranked Subtracted 224.763 14.197 210.566
    SLC16A1 monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] Measured 10348.5 858.2 11206.7
    TMEM33 db83 protein. [swissprot;acc:p57088] Rooted High confidence 33.9632 15.5377 18.4255

    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/