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 [...,...].
    description Rank Gene Hugo Value Type Network Comparison Type Interaction Map red Filtered network_comparison green
    Results: HTML CSV LaTeX Showing element 432 to 481 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 2672 BCAT1 210.957 1.00102 210.741
    branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] 2687 BCAT2 210.939 1.00087 210.755
    brca1 associated protein. [refseq;acc:nm_006768] 3161 BRAP 0.00001 1 0.00001
    brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 1752 BARD1 216.271 1.01258 218.991
    brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 294 BCCIP 240.782 1.10356 265.717
    breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 229 BCAR3 226.401 1.12028 202.094
    breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 939 BRCA1 216.501 1.03588 224.27
    breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 691 BCAS2 217.602 1.05532 206.195
    brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 2713 ARFGEF1 220.521 1.00057 220.395
    brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] 2711 ARFGEF2
    brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 945 ARID1B 212.44 1.03586 205.085
    bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4] 3149 BRPF3 0.00001 1 0.00001
    bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] 2747 BRD7 201.477 1.00018 201.514
    bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696] 3139 BRD1 0.00001 1 0.00001
    bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 2241 BRD2 222.96 1.00618 224.338
    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 1 0.00001
    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 1.07821 246.33
    bup protein. [refseq;acc:nm_012071] 2911 COMMD3 0.00001 1 0.00001
    bystin. [swissprot;acc:q13895] 1149 BYSL 239.505 1.0271 233.185
    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 1.01223 231.732
    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 1.003 217.991
    c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363] 1554 CTBP1 196.215 1.01656 193.018
    c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] 1558 CTBP2 196.171 1.01655 192.977
    c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 844 CLEC3A 178.033 1.04223 170.82
    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 1.00298 217.571
    c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 1625 RPUSD2 217.446 1.01515 214.2
    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 1.01807 208.339
    c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 321 no value 241.892 1.09949 265.959
    c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 260 HS3ST6 219.421 1.11394 196.978
    ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 2577 CANT1 192.625 1.00154 192.922
    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 1.01988 222.117
    cab2. [refseq;acc:nm_033419] 769 PERLD1 210.946 1.04873 221.225
    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 1.01146 215.323
    cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517] 1526 FAT 219.306 1.01766 223.179
    calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] 1330 RCAN1 218.508 1.02275 213.648
    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 1.00284 195.08
    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 1.03586 205.088
    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 1.02889 203.183
    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 1.00673 214.481
    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 1.06577 207.121
    calmegin precursor. [swissprot;acc:o14967] 1909 CLGN 217.48 1.01033 215.256
    calmodulin. [swissprot;acc:p02593] 2928 no value 0.00001 1 0.00001

    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/