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 2101 to 2150 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Value Type
    		Interaction Map
    		red
    		network_comparison
    		green
    263 HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Ranked High confidence 219.421 1.11394 196.978
    KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Measured 24896.4 1.21852 20431.7
    PXN paxillin. [swissprot;acc:p49023] Rooted 59.4073 1.12276 66.7002
    STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Measured Low confidence 7424.14 1.06106 7877.49
    264 ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Squared High confidence 26157.6 1.29261 20236.2
    BICD1 bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] Rooted Low confidence 70.75 1.05603 74.7143
    C16orf70 upf0183 protein. [swissprot;acc:q9bsu1] Squared 43982.2 1.08984 40356.7
    COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Measured High confidence 4987.58 1.2181 4094.57
    DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked 219.421 1.11394 196.978
    DGKQ diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Measured Low confidence 6396.44 1.06105 6786.96
    LEO1 senescence downregulated leo1-like. [refseq;acc:nm_138792] Ranked 216.546 1.0458 207.063
    WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Rooted High confidence 66.1122 1.12148 74.1438
    265 KIF3A kinesin-like protein kif3a (microtubule plus end-directed kinesin motor 3a). [swissprot;acc:q9y496] Squared Low confidence 47740.4 1.0897 43810.6
    LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] High confidence 26157.6 1.29261 20236.2
    LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted 56.031 1.12131 62.8281
    SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Ranked 225.217 1.11241 202.459
    SLC9A7 solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [refseq;acc:nm_032591] Low confidence 216.546 1.0458 207.063
    SYNJ2 synaptojanin 2 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 2) (fragment). [swissprot;acc:o15056] Measured 8081.02 1.06098 8573.8
    TFIP11 tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted 70.75 1.05603 74.7143
    WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured High confidence 24806.9 1.21782 20369.9
    266 CPA1 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Low confidence 8817.03 1.06089 9353.9
    CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 24806.9 1.21782 20369.9
    CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted 66.1064 1.12103 74.1074
    FEM1B fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Squared 26157.6 1.29261 20236.2
    OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted Low confidence 66.2701 1.05595 69.978
    RPS25 40s ribosomal protein s25. [swissprot;acc:p25111] Squared 48481.4 1.08937 44504.2
    SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked High confidence 241.07 1.11121 267.88
    WDR92 calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] Low confidence 214.887 1.04563 205.509
    267 ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Rooted High confidence 66.1064 1.12103 74.1073
    CCDC22 jm1 protein. [refseq;acc:nm_014008] Low confidence 67.162 1.05588 70.9153
    CEPT1 choline/ethanolaminephosphotransferase. [refseq;acc:nm_006090] Measured 8813.83 1.06069 9348.71
    DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Ranked High confidence 241.07 1.11121 267.88
    LRRC3 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Squared 26157.6 1.29261 20236.2
    RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured 14021.4 1.21682 11523
    TNS1 tensin. [refseq;acc:nm_022648] Ranked Low confidence 215.258 1.04559 205.872
    XKR7 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Squared 33343.5 1.08857 36296.7
    268 no value proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted High confidence 66.1064 1.12103 74.1074
    CDKL1 serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] Low confidence 70.9046 1.05585 74.8645
    CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Measured High confidence 24473.9 1.21593 20127.8
    EIF5 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked 271.016 1.10996 244.167
    EXO1 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Squared Low confidence 51352 1.08816 47191.4
    LAMC1 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] High confidence 26157.6 1.29261 20236.2
    RECK reversion-inducing cysteine-rich protein with kazal motifs precursor (hreck) (suppressor of tumorigenicity 15) (st15). [swissprot;acc:o95980] Measured Low confidence 8813.83 1.06069 9348.71
    SOAT2 sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] Ranked 208.469 1.04519 199.455
    269 CHPT1 choline phosphotransferase 1; cholinephosphotransferase 1 alpha; cholinephosphotransferase 1. [refseq;acc:nm_020244] Measured 8813.95 1.06069 9348.9
    FABP7 fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Squared 50001.6 1.08807 45954.4
    HCK tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Rooted High confidence 66.1064 1.12103 74.1074
    LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured 4590.18 1.21466 5575.52
    PCYT1A cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Ranked 241.373 1.10763 267.352
    SLC46A2 thymic stromal co-transporter. [refseq;acc:nm_033051] Squared 26157.6 1.29261 20236.2

    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/