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 Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 3051 to 3100 of 66312 in total
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    191 px serine/threonine kinase. [refseq;acc:nm_017771] PXK Ranked Subtracted Low confidence 196.372 206.947 10.575
    ras-related protein rab-37. [swissprot;acc:q96ax2] RAB37 Measured 10730.1 10148.2 581.9
    similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] AGBL3 Divided 9385.4 10086.4 1.07469
    sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] SPHK1 Squared Subtracted High confidence 42411.6 55802.1 13390.5
    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 Divided 4638.1 5923.4 1.27712
    tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226] TPM4 Rooted Subtracted Low confidence 70.8512 75.1709 4.3197
    192 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] ARAF Measured Divided High confidence 17757.5 14008 1.26767
    aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] AQP2 Squared 71387.4 96033.4 1.34524
    bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] no value Ranked Subtracted Low confidence 196.372 206.947 10.575
    chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] CHRAC1 Measured 5674.92 6255.18 580.26
    dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] DUOX2 Rooted 69.8853 74.201 4.3157
    leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] SHOC2 Squared Divided 51506.6 46445.8 1.10896
    ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] LGTN Ranked Subtracted High confidence 241.373 267.352 25.979
    membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] RC3H2 Divided Low confidence 217.341 206.571 1.05214
    musashi 2 isoform a. [refseq;acc:nm_138962] MSI2 High confidence 227.491 199.458 1.14055
    nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] NOX5 Rooted Low confidence 69.9161 74.2187 1.06154
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 Subtracted High confidence 116.792 106.107 10.685
    small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] no value Measured 10807.4 12338.5 1531.1
    splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] SF4 Rooted Divided 53.6107 61.5862 1.14877
    transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] KRAS Squared Subtracted Low confidence 51551.5 46457.1 5094.4
    trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] TRMU Measured Divided 9385.4 10086.4 1.07469
    udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] DPAGT1 Squared Subtracted High confidence 42411.6 55802.1 13390.5
    193 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] PAPSS1 Ranked 241.373 267.352 25.979
    cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] no value Measured Low confidence 5752.65 6330.03 577.38
    dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] DUOX1 Rooted 69.8912 74.2044 4.3132
    hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] HEYL Squared 52187.1 47109.7 5077.4
    hbs1-like. [refseq;acc:nm_006620] HBS1L Ranked Divided 206.166 216.913 1.05213
    lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] MIP Squared High confidence 71386.9 96032.5 1.34524
    musashi 1. [refseq;acc:nm_002442] MSI1 Ranked 227.491 199.458 1.14055
    nadph oxidase 4. [refseq;acc:nm_016931] NOX4 Rooted Low confidence 69.9166 74.219 1.06154
    nostrin. [refseq;acc:nm_052946] NOSTRIN High confidence 59.6399 51.9242 1.1486
    raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] RAF1 Measured 17756.5 14007.3 1.26766
    rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] DLC1 Squared Subtracted 42411.6 55802.1 13390.5
    serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] PPP2R5E Rooted 116.707 106.044 10.663
    serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] PPP2R1A Measured 4612.39 3093.6 1518.79
    star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] STARD7 Divided Low confidence 6534.34 7021.2 1.07451
    testis specific, 10. [refseq;acc:nm_025244] TSGA10 Ranked Subtracted 196.373 206.946 10.573
    transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] HRAS Squared Divided 51484.4 46440.2 1.10862
    194 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 Rooted Subtracted 71.0652 75.377 4.3118
    aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] AQP1 Squared Divided High confidence 71346.6 95965.1 1.34505
    conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] COG5 Ranked Low confidence 215.723 205.046 1.05207
    cyclin g2. [swissprot;acc:q16589] CCNG2 Measured High confidence 17738.6 13995.7 1.26743
    Rooted Subtracted 116.707 106.044 10.663
    eap30 subunit of ell complex. [refseq;acc:nm_007241] SNF8 Divided 59.6399 51.9242 1.1486
    huntingtin interacting protein c. [refseq;acc:nm_012272] PRPF40B Measured Subtracted 4300.47 5807.72 1507.25
    map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] MAPKAPK2 Squared 42411.6 55802.1 13390.5
    nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] NOX3 Rooted Divided Low confidence 69.9164 74.2188 1.06154
    nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] POR Ranked Subtracted High confidence 241.373 267.352 25.979
    nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 Divided 227.491 199.458 1.14055
    rab11-family interacting protein 4. [refseq;acc:nm_032932] RAB11FIP4 Subtracted Low confidence 183.27 172.702 10.568

    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/