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 [...,...].
    Gene Rank Value Type Hugo Network Comparison Type description Interaction Map Filtered network_comparison red green
    Results: HTML CSV LaTeX Showing element 1262 to 1311 of 66312 in total
    Filtered  : 1
    Rank
    		Value Type
    		Hugo
    		Network Comparison Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    79 Rooted no value Subtracted homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 6.954 101.348 108.302
    NEURL neuralized-like. [refseq;acc:nm_004210] High confidence 16.2549 27.9107 44.1656
    SLC7A11 Divided cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Low confidence 1.0978 68.7629 75.4877
    80 Measured no value protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] 1.11235 5334.13 5933.4
    HOXA5 Subtracted homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] High confidence 3690.3 20446.1 24136.4
    MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Low confidence 966.8 11285.3 10318.5
    TIA1 Divided nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] High confidence 1.43834 4133.47 5945.32
    Ranked no value Subtracted transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Low confidence 18.464 226.338 207.874
    CACNG4 Divided voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] High confidence 1.25669 254.691 202.668
    RINT1 rad50-interacting protein 1. [refseq;acc:nm_021930] Low confidence 1.09499 221.194 202.005
    SON Subtracted son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] High confidence 51.491 294.053 242.562
    Squared BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 47102.7 117515 70412.3
    PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Low confidence 11528.6 69693.1 58164.5
    PPP2R5E Divided 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] High confidence 1.66962 117718 70505.9
    TEGT bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] Low confidence 1.23446 281799 228277
    Rooted HSD17B14 Subtracted retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 6.954 101.348 108.302
    JUNB transcription factor jun-b. [swissprot;acc:p17275] High confidence 16.1138 63.4173 79.5311
    PPP2R2B Divided serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 1.32368 63.7477 48.1594
    SLC7A6 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Low confidence 1.0978 68.7629 75.4877
    81 Measured no value Subtracted homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 3690.3 20446.1 24136.4
    NDN necdin. [swissprot;acc:q99608] Low confidence 966.8 11285.3 10318.5
    RGS12 Divided regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] 1.11183 5528.68 6146.97
    TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] High confidence 1.43691 4136.36 5943.56
    Ranked CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 1.25645 254.614 202.646
    HOMER2 Subtracted homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 50.355 252.371 202.016
    RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Low confidence 18.394 247.087 228.693
    TFDP2 Divided transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 1.09286 227.623 208.281
    Squared no value Subtracted ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 10442.9 60862.1 50419.2
    CCNG2 Divided cyclin g2. [swissprot;acc:q16589] High confidence 1.66962 117718 70505.9
    RHBDL1 rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783] Low confidence 1.23446 281799 228277
    ZNF547 Subtracted sedlin. [swissprot;acc:o14582] High confidence 44213 112820 157033
    Rooted no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Low confidence 6.8009 59.2532 66.0541
    guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] High confidence 16.0593 40.3337 24.2744
    EIF4B Divided eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Low confidence 1.0978 68.7629 75.4877
    PPP2R2C serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] High confidence 1.32362 63.7475 48.1615
    82 Measured HSD17B14 Subtracted retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 3690.3 20446.1 24136.4
    LASS2 Divided lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Low confidence 1.1108 7098.44 7884.98
    MAGED1 Subtracted melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 966.8 11285.3 10318.5
    SNRPD1 Divided small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] High confidence 1.42694 4172.91 5954.48
    Ranked COQ7 Subtracted ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 50.325 252.329 202.004
    DGKH Divided diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Low confidence 1.09085 226.981 208.077
    GNB5 guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence 1.25304 267.636 335.359
    TAF2 Subtracted tbp-associated factor 2; taf2 rna polymerase ii, tata box binding protein (tbp)-associated factor, 150 kd; tata box binding protein (tbp)-associated factor, rna polymerase ii, b, 150kd; cofactor of initiator function, 150kd subunit. [refseq;acc:nm_003184] Low confidence 18.338 237.567 219.229
    Squared no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 10343.7 60811 50467.3
    synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] High confidence 44213 112820 157033
    CCNG1 Divided cyclin g1 (cyclin g). [swissprot;acc:p51959] 1.66962 117718 70505.8
    GMPPA gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Low confidence 1.22949 75927.4 61755.3
    Rooted ATF3 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] High confidence 1.30768 60.8022 79.5099
    GNG12 Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 16.0593 40.3337 24.2744
    SLC7A9 Divided b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Low confidence 1.0978 68.7629 75.4877

    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/