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 description Value Type Interaction Map Filtered red network_comparison green
    Results: HTML CSV LaTeX Showing element 59974 to 60023 of 66312 in total
    Interaction Map  : Low confidence
    Filtered  : 1
    Rank
    		Network Comparison Type
    		Hugo
    		description
    		Value Type
    		red
    		network_comparison
    		green
    4269 Subtracted PFKFB1 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (6pf-2-k/fru- 2,6-p2ase liver isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:p16118] Measured 8966.91 169.06 8797.85
    ZBTB7B kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] Ranked 202.346 1.904 200.442
    ZSCAN21 zinc finger protein 38 homolog (zfp-38) (ny-ren-21 antigen). [swissprot;acc:q9y5a6] Rooted 76.1821 1.8642 78.0463
    4270 Divided CAMK2G calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] Squared 45840.4 1.02478 44732
    TAS1R1 krueppel-related zinc finger protein 3 (hkr3 protein). [swissprot;acc:p10074] Rooted 76.182 1.02447 78.0463
    UGT1A9 udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [swissprot;acc:p19224] Ranked 206.898 1.00942 204.968
    ZNF806 zinc finger protein 285. [refseq;acc:nm_152354] Measured 9143.34 1.01967 9323.19
    Subtracted no value similar to zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [refseq;acc:nm_145233] Rooted 76.1821 1.8642 78.0463
    DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Measured 8966.91 169.06 8797.85
    SLCO4A1 solute carrier family 21 member 12 (sodium-independent organic anion transporter e) (organic anion transporting polypeptide e) (oatp-e) (colon organic anion transporter) (organic anion transporter polypeptide-related protein 1) (oatp-rp1) (oatprp1) (poat). [swissprot;acc:q96bd0] Squared 49855 1082.7 50937.7
    UGT8 2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (ec 2.4.1.45) (udp-galactose-ceramide galactosyltransferase) (ceramide udp-galactosyltransferase) (cerebroside synthase). [swissprot;acc:q16880] Ranked 207 1.903 205.097
    4271 Divided no value zinc finger protein 257 (bone marrow zinc finger 4) (bmzf-4). [swissprot;acc:q9y2q1] Measured 9143.34 1.01967 9323.19
    zinc finger protein zfd25. [swissprot;acc:q9uii5] Rooted 76.1821 1.02447 78.0464
    CAMK2A calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7] Squared 45840.6 1.02478 44732.1
    UGT2B4 udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] Ranked 206.877 1.00942 204.946
    Subtracted HDAC4 histone deacetylase 4 (hd4). [swissprot;acc:p56524] Squared 49854.5 1082.4 50936.9
    PFKFB2 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (6pf-2-k/fru- 2,6-p2ase heart-type isozyme) (pfk-2/fbpase-2) [includes: 6- phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:o60825] Measured 8966.91 169.06 8797.85
    SH3GLB2 sh3-containing protein sh3glb2; sh3-domain, grb2-like, endophilin b2. [refseq;acc:nm_020145] Ranked 203.11 1.902 205.012
    ZNF233 zinc finger protein 233. [refseq;acc:nm_181756] Rooted 76.1821 1.8642 78.0463
    4272 Divided HKR1 krueppel-related zinc finger protein 1 (hkr1 protein). [swissprot;acc:p10072] Measured 9143.34 1.01967 9323.19
    NCK1 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Squared 46064.5 1.02477 44951.2
    SNX6 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Ranked 201.271 1.00942 199.393
    ZNF738 zinc finger protein 431. [swissprot;acc:q8tf32] Rooted 76.1821 1.02447 78.0464
    Subtracted GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Ranked 201.502 1.902 199.6
    HDAC9 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] Squared 49854.4 1082.4 50936.8
    PFKFB4 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 (6pf-2-k/fru- 2,6-p2ase testis-type isozyme) [includes: 6-phosphofructo-2-kinase (ec 2.7.1.105); fructose-2,6-bisphosphatase (ec 3.1.3.46)]. [swissprot;acc:q16877] Measured 8966.91 169.06 8797.85
    ZNF222 zinc finger protein 222. [swissprot;acc:q9uk12] Rooted 76.1821 1.8642 78.0463
    4273 Divided no value f23269_2. [sptrembl;acc:o75290] 1.02447 78.0464
    SRP54 signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] Squared 46499.2 1.02476 45375.8
    UGT2B10 udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] Ranked 206.877 1.00942 204.946
    ZFP41 zinnc finger protein gli4 (krueppel-related zinc finger protein 4) (hkr4 protein). [swissprot;acc:p10075] Measured 9143.32 1.01967 9323.18
    Subtracted GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Ranked 201.502 1.902 199.6
    MAP3K7IP1 mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] Squared 45584.4 1082.1 44502.3
    NEK1 serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Measured 7682.95 169.05 7852
    RBAK rb-associated krab repressor. [refseq;acc:nm_021163] Rooted 76.1821 1.8642 78.0463
    4274 Divided no value dj54b20.4 (novel krab box containing c2h2 type zinc finger protein). [sptrembl;acc:q96qh7] 1.02447 78.0464
    udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] Ranked 206.887 1.00941 204.958
    zinc finger protein 273 (zinc finger protein hzf9) (fragment). [swissprot;acc:q14593] Measured 9143.34 1.01967 9323.19
    MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Squared 45066.7 1.02468 43981.4
    Subtracted ABCD3 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] Ranked 202.428 1.902 204.33
    CDC123 d123 gene product. [refseq;acc:nm_006023] Squared 45815.3 1081.9 44733.4
    ZIM3 zinc finger imprinted 3. [swissprot;acc:q96pe6] Rooted 76.1821 1.8642 78.0463
    ZNF394 zinc finger protein 99. [refseq;acc:nm_032164] Measured 7963.3 168.85 8132.15
    4275 Divided no value similar to zinc finger protein 136. [refseq;acc:nm_145295] Rooted 76.1821 1.02447 78.0464
    zinc finger protein 345 (zinc finger protein hzf10). [swissprot;acc:q14585] Measured 9143.35 1.01967 9323.2
    DNAJB11 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] Squared 45066.7 1.02468 43981.4
    UGT2A1 udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798] Ranked 206.895 1.00941 204.967
    Subtracted no value zinc finger protein 187. [refseq;acc:nm_152736] Rooted 76.1821 1.8642 78.0463
    SH3GLB1 sh3-containing protein sh3glb1; sh3-containing protein sh3glb1; cgi-61 protein; endophilin b1; endophilin b1; bax-interacting factor 1; sh3-domain, grb2-like, endophilin b1. [refseq;acc:nm_016009] Ranked 203.11 1.902 205.012
    ZBTB20 zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] Squared 43030.7 1080.9 41949.8

    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/