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 description Rank Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 444 to 493 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		green
    		network_comparison
    bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 2747 BRD7 201.477 201.514 1.00018
    bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 BRD1 0.00001 0.00001 1
    bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 2241 BRD2 222.96 224.338 1.00618
    bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 2237 BRD3 222.965 224.343
    bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] 2238 BRD4 222.959 224.337
    bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7] 3214 NUB1 0.00001 0.00001 1
    bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 449 DST 228.463 246.33 1.07821
    bup protein. [refseq;acc:nm_012071] 2911 COMMD3 0.00001 0.00001 1
    bystin. [swissprot;acc:q13895] 1149 BYSL 239.505 233.185 1.0271
    c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 1766 MTHFD1 228.932 231.732 1.01223
    c-jun-amino-terminal kinase interacting protein 3 (jnk-interacting protein 3) (jip-3) (jnk map kinase scaffold protein 3) (mitogen- activated protein kinase 8-interacting protein 3). [swissprot;acc:q9upt6] 2473 MAPK8IP3 218.644 217.991 1.003
    c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1554 CTBP1 196.215 193.018 1.01656
    c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1558 CTBP2 196.171 192.977 1.01655
    c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 844 CLEC3A 178.033 170.82 1.04223
    c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 2475 TENC1 218.219 217.571 1.00298
    c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 1625 RPUSD2 217.446 214.2 1.01515
    c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 1506 C16orf42 212.103 208.339 1.01807
    c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 321 no value 241.892 265.959 1.09949
    c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 260 HS3ST6 219.421 196.978 1.11394
    ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 2577 CANT1 192.625 192.922 1.00154
    caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] 1448 ZMPSTE24 226.532 222.117 1.01988
    cab2. [refseq;acc:nm_033419] 769 PERLD1 210.946 221.225 1.04873
    cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] 1829 CAD 212.884 215.323 1.01146
    cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] 1526 FAT 219.306 223.179 1.01766
    calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 1330 RCAN1 218.508 213.648 1.02275
    calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] 1328 RCAN2 218.509 213.649
    calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] 1331 RCAN3
    calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] 2494 SLC25A12 194.527 195.08 1.00284
    calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] 2497 SLC25A13
    calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 940 CAPNS1 212.442 205.088 1.03586
    calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 1100 ATP2C1 209.052 203.183 1.02889
    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] 2172 CAMK2A 215.925 214.481 1.00673
    calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] 2173 CAMK2B
    calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] 2162 CAMK2D
    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] 2161 CAMK2G
    calcyphosine. [swissprot;acc:q13938] 563 CAPS 220.744 207.121 1.06577
    calmegin precursor. [swissprot;acc:o14967] 1909 CLGN 217.48 215.256 1.01033
    calmodulin. [swissprot;acc:p02593] 2928 no value 0.00001 0.00001 1
    calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 1910 CANX 217.48 215.256 1.01033
    calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 299 CAPN1 268.635 243.592 1.10281
    calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 298 CAPN2 268.632 243.588
    calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 2181 CALR 227.117 225.62 1.00664
    calsyntenin-1 precursor. [swissprot;acc:o94985] 2699 CLSTN1 188.435 188.31 1.00066
    calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 2705 CLSTN2 188.457 188.334 1.00065
    calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 2706 CLSTN3 188.459 188.336
    camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1363 CREB5 218.591 213.899 1.02194
    camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 CREBL2 0.00001 0.00001 1
    camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644] 3089 PRKAR1A
    camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 2307 PRKAR2A 215.554 214.467 1.00507
    camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 2313 PRKAR2B 215.529 214.449 1.00504

    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/