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 network_comparison red green
    Results: HTML CSV LaTeX Showing element 630 to 679 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		Hugo
    		Value Type
    		description
    		Interaction Map
    		network_comparison
    		red
    		green
    79 RHBDL3 Squared rhomboid-related protein 4 (ec 3.4.21.-) (ventrhoid transmembrane protein). [swissprot;acc:p58872] Low confidence 1.23446 281799 228277
    SLC7A11 Rooted cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] 1.0978 68.7629 75.4877
    UFC1 Measured protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 1.48558 3074.57 4567.51
    80 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] Low confidence 1.11235 5334.13 5933.4
    CACNG4 Ranked 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
    PPP2R2B Rooted 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
    PPP2R5E Squared 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] 1.66962 117718 70505.9
    RINT1 Ranked rad50-interacting protein 1. [refseq;acc:nm_021930] Low confidence 1.09499 221.194 202.005
    SLC7A6 Rooted solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] 1.0978 68.7629 75.4877
    TEGT Squared bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] 1.23446 281799 228277
    TIA1 Measured 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
    81 CACNG5 Ranked voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 1.25645 254.614 202.646
    CCNG2 Squared cyclin g2. [swissprot;acc:q16589] 1.66962 117718 70505.9
    EIF4B Rooted 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
    RGS12 Measured regulator of g-protein signaling 12 (rgs12). [swissprot;acc:o14924] Low confidence 1.11183 5528.68 6146.97
    RHBDL1 Squared rhomboid-related protein 1 (ec 3.4.21.-) (rrp) (rhomboid-like protein 1). [swissprot;acc:o75783] 1.23446 281799 228277
    TFDP2 Ranked transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 1.09286 227.623 208.281
    TIAL1 Measured nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] High confidence 1.43691 4136.36 5943.56
    82 ATF3 Rooted cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 1.30768 60.8022 79.5099
    CCNG1 Squared cyclin g1 (cyclin g). [swissprot;acc:p51959] 1.66962 117718 70505.8
    DGKH Ranked diacylglycerol kinase, eta isoform 1. [refseq;acc:nm_152910] Low confidence 1.09085 226.981 208.077
    GMPPA Squared gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] 1.22949 75927.4 61755.3
    GNB5 Ranked guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence 1.25304 267.636 335.359
    LASS2 Measured lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Low confidence 1.1108 7098.44 7884.98
    SLC7A9 Rooted b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] 1.0978 68.7629 75.4877
    SNRPD1 Measured 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
    83 DGKD Ranked diacylglycerol kinase, delta (ec 2.7.1.107) (diglyceride kinase) (dgk-delta) (dag kinase delta) (130 kda diacylglycerol kinase) (fragment). [swissprot;acc:q16760] Low confidence 1.09085 226.981 208.077
    DVL1 Measured segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 1.10869 7030.67 7794.8
    FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] High confidence 1.42597 4932.27 7033.29
    MAGED4 Ranked melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 1.24949 88.2482 110.265
    NFU1 Squared hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Low confidence 1.22607 60583.7 74280
    PPP2R1B Rooted serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] High confidence 1.30666 63.6507 48.7127
    PPP2R5A Squared serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 1.66962 117718 70505.9
    STARD7 Rooted star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Low confidence 1.09753 61.8872 67.9229
    84 no value Measured jun dimerization protein. [refseq;acc:nm_130469] High confidence 1.42597 4932.27 7033.29
    Ranked transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Low confidence 1.08882 226.338 207.874
    Rooted 1.09638 62.4962 68.5193
    BRAF Squared b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] High confidence 1.66896 117515 70412.3
    MAGEE2 Ranked hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 1.24949 88.2482 110.265
    NCL Squared nucleolin (protein c23). [swissprot;acc:p19338] Low confidence 1.20735 70162 58112.6
    NFYC Rooted nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] High confidence 1.30362 46.7419 60.9337
    SEPT4 Measured septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Low confidence 1.10857 11141.5 12351.1
    85 no value Ranked melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] High confidence 1.24949 88.2482 110.265
    Squared ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Low confidence 1.20712 60862.1 50419.2
    ATG12 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] High confidence 1.65709 67438.6 40697
    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 1.09453 61.1174 66.8946
    DVL2 Measured segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 1.10843 7034.43 7797.14
    FOSL2 fos-related antigen 2. [swissprot;acc:p15408] High confidence 1.42395 4941.95 7037.11
    KCND2 Ranked potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Low confidence 1.08671 225.735 245.308

    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/