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 red network_comparison green
    Results: HTML CSV LaTeX Showing element 1780 to 1829 of 66312 in total
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		red
    		network_comparison
    		green
    112 Divided LASS2 Rooted lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Low confidence 71.084 1.08102 76.8432
    MAGEE2 Measured hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 11285.3 1.0937 10318.5
    MYH3 Squared myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] High confidence 19321 1.54043 12542.6
    PBK Ranked 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] 332.874 1.24557 267.246
    SNRP70 Measured u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 4366.44 1.35116 5899.76
    Subtracted AGL Squared 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] Low confidence 61349.6 8501.2 52848.4
    ATG12 Measured autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] High confidence 11757.8 2405.69 9352.11
    CTPS2 Squared cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 96730.5 27443.8 69286.7
    DLGAP4 Ranked disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Low confidence 197.779 14.204 211.983
    POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] High confidence 275.754 39.846 235.908
    RASAL2 Rooted ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Low confidence 55.9786 5.8855 61.8641
    SLC16A5 Measured monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] 10351.8 859 11210.8
    SMPD2 Rooted 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] High confidence 33.9632 15.5377 18.4255
    113 Divided no value Measured filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 4366.44 1.35116 5899.76
    melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Low confidence 11285.3 1.0937 10318.5
    ARRB2 Rooted beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] High confidence 80.4705 1.26165 101.526
    CREG2 Ranked cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Low confidence 197.763 1.07205 212.011
    KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 332.874 1.24557 267.246
    MAN1B1 Rooted 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] Low confidence 66.9562 1.08017 72.3243
    MYH1 Squared myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] High confidence 19321 1.54043 12542.6
    SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Low confidence 59884.7 1.14972 68850.8
    Subtracted ATF3 Measured cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence 4800.81 2331.9 7132.71
    BRP44 Squared brain protein 44. [swissprot;acc:o95563] Low confidence 62640.6 8397.7 71038.3
    CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] High confidence 96602.7 27391.5 69211.2
    PPP2CA Ranked serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 194.372 39.832 234.204
    SLC11A2 natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Low confidence 224.763 14.197 210.566
    SLC16A1 Measured monocarboxylate transporter 1 (mct 1). [swissprot;acc:p53985] 10348.5 858.2 11206.7
    TMEM33 Rooted db83 protein. [swissprot;acc:p57088] High confidence 33.9632 15.5377 18.4255
    VPS33B vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 69.4249 5.8215 75.2464
    114 Divided no value Squared myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] High confidence 19321 1.54043 12542.6
    ARRB1 Rooted beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 80.4705 1.26165 101.526
    DLGAP1 Ranked 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] Low confidence 197.779 1.07182 211.983
    KHDRBS1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 332.874 1.24557 267.246
    MAGEA11 Measured melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Low confidence 11285.3 1.0937 10318.5
    OTC Squared ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 65896.9 1.14832 75670.5
    PRPF40B Measured huntingtin interacting protein c. [refseq;acc:nm_012272] High confidence 4300.47 1.35048 5807.72
    PSEN2 Rooted presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Low confidence 66.9562 1.08017 72.3243
    Subtracted no value Measured cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] High confidence 13768.2 2302.2 11466
    ATG12 Squared autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 67438.6 26741.6 40697
    B9D1 Ranked b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 37.447 267.265
    DFFB Rooted dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Low confidence 61.1174 5.7772 66.8946
    GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence 40.225 15.5199 24.7051
    MRPS17 Ranked 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 58 14 44
    SLC16A5 Squared monocarboxylate transporter 6 (mct 6) (mct 5). [swissprot;acc:o15375] 62486.3 8239.3 70725.6
    SLC16A7 Measured monocarboxylate transporter 2 (mct 2). [swissprot;acc:o60669] 10346.9 857.9 11204.8
    115 Divided CPSF2 Squared cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 59004.9 1.14691 51446.9
    DLGAP4 Ranked disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] 197.779 1.07182 211.983
    FBXW7 Rooted f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 66.9562 1.08017 72.3243
    KHDRBS2 Ranked kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence 332.874 1.24557 267.246
    MAGEA2B Measured melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Low confidence 11285.3 1.0937 10318.5

    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/