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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2101 to 2150 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    263 p10-binding protein. [refseq;acc:nm_024491] Squared Low confidence 52319.1 48005.3 1.08986
    paxillin. [swissprot;acc:p49023] Rooted High confidence 59.4073 66.7002 1.12276
    sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [swissprot;acc:q92581] Ranked Low confidence 216.546 207.063 1.0458
    trs85 homolog. [swissprot;acc:q9y2l5] Measured High confidence 24896.4 20431.7 1.21852
    264 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Squared 26157.6 20236.2 1.29261
    bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714] Rooted Low confidence 70.75 74.7143 1.05603
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Measured High confidence 4987.58 4094.57 1.2181
    diacylglycerol kinase, theta (ec 2.7.1.107) (diglyceride kinase) (dgk- theta) (dag kinase theta). [swissprot;acc:p52824] Low confidence 6396.44 6786.96 1.06105
    mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked High confidence 219.421 196.978 1.11394
    senescence downregulated leo1-like. [refseq;acc:nm_138792] Low confidence 216.546 207.063 1.0458
    upf0183 protein. [swissprot;acc:q9bsu1] Squared 43982.2 40356.7 1.08984
    wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Rooted High confidence 66.1122 74.1438 1.12148
    265 kinesin-like protein kif3a (microtubule plus end-directed kinesin motor 3a). [swissprot;acc:q9y496] Squared Low confidence 47740.4 43810.6 1.0897
    leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] High confidence 26157.6 20236.2 1.29261
    solute carrier family 9, member 7; nonselective sodium potassium/proton exchanger; sodium/hydrogen exchanger 7. [refseq;acc:nm_032591] Ranked Low confidence 216.546 207.063 1.0458
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] High confidence 225.217 202.459 1.11241
    synaptojanin 2 (ec 3.1.3.36) (synaptic inositol-1,4,5-trisphosphate 5- phosphatase 2) (fragment). [swissprot;acc:o15056] Measured Low confidence 8081.02 8573.8 1.06098
    tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted 70.75 74.7143 1.05603
    u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] High confidence 56.031 62.8281 1.12131
    wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 24806.9 20369.9 1.21782
    266 40s ribosomal protein s25. [swissprot;acc:p25111] Squared Low confidence 48481.4 44504.2 1.08937
    calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] Ranked 214.887 205.509 1.04563
    carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Measured 8817.03 9353.9 1.06089
    cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 24806.9 20369.9 1.21782
    fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Squared 26157.6 20236.2 1.29261
    odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Rooted Low confidence 66.2701 69.978 1.05595
    proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] High confidence 66.1064 74.1074 1.12103
    transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked 241.07 267.88 1.11121
    267 choline/ethanolaminephosphotransferase. [refseq;acc:nm_006090] Measured Low confidence 8813.83 9348.71 1.06069
    density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Ranked High confidence 241.07 267.88 1.11121
    dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Squared Low confidence 33343.5 36296.7 1.08857
    jm1 protein. [refseq;acc:nm_014008] Rooted 67.162 70.9153 1.05588
    leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Squared High confidence 26157.6 20236.2 1.29261
    ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured 14021.4 11523 1.21682
    tensin. [refseq;acc:nm_022648] Ranked Low confidence 215.258 205.872 1.04559
    tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Rooted High confidence 66.1064 74.1073 1.12103
    268 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Measured 24473.9 20127.8 1.21593
    eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked 271.016 244.167 1.10996
    exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Squared Low confidence 51352 47191.4 1.08816
    laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] High confidence 26157.6 20236.2 1.29261
    proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 66.1064 74.1074 1.12103
    reversion-inducing cysteine-rich protein with kazal motifs precursor (hreck) (suppressor of tumorigenicity 15) (st15). [swissprot;acc:o95980] Measured Low confidence 8813.83 9348.71 1.06069
    serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532] Rooted 70.9046 74.8645 1.05585
    sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] Ranked 208.469 199.455 1.04519
    269 choline phosphotransferase 1; cholinephosphotransferase 1 alpha; cholinephosphotransferase 1. [refseq;acc:nm_020244] Measured 8813.95 9348.9 1.06069
    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 High confidence 241.373 267.352 1.10763
    fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Squared Low confidence 50001.6 45954.4 1.08807
    spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Rooted 70.8256 74.7762 1.05578
    sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610] Ranked 208.436 199.44 1.04511
    thymic stromal co-transporter. [refseq;acc:nm_033051] Squared High confidence 26157.6 20236.2 1.29261

    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
    - 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/