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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1608 to 1657 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    coronin-like protein p57 (coronin 1a). [swissprot;acc:p31146] 2220 CORO1A Low confidence 202.493 198.725 1.01896
    corticosteroid 11-beta-dehydrogenase, isozyme 1 (ec 1.1.1.146) (11-dh) (11-beta-hydroxysteroid dehydrogenase 1) (11-beta-hsd1). [swissprot;acc:p28845] 2033 HSD11B1 202.411 206.338 1.0194
    cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] 564 COX15 203.197 197.076 1.03106
    1513 High confidence 213.268 209.509 1.01794
    cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] 1168 CXXC1 219.399 213.784 1.02626
    1615 Low confidence 205.179 200.988 1.02085
    cpz gene product. [refseq;acc:nm_003652] 716 CPZ High confidence 223.121 211.685 1.05402
    3441 Low confidence 201.285 198.273 1.01519
    craniofacial development protein 1; phosphoprotein (bucentaur). [refseq;acc:nm_006324] 2782 CFDP1 200.078 196.657 1.0174
    creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] 1940 CKB High confidence 198.19 196.252 1.00988
    3691 Low confidence 200.632 197.897 1.01382
    creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] 1971 CKM High confidence 198.258 196.346 1.00974
    3683 Low confidence 200.659 197.918 1.01385
    creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] 1936 CKMT2 High confidence 198.3 196.347 1.00995
    3677 Low confidence 200.663 197.919 1.01386
    creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 1938 no value High confidence 198.293 196.341 1.00994
    3675 Low confidence 200.661 197.918 1.01386
    crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 284 BCAR1 High confidence 224.657 203.235 1.10541
    1119 Low confidence 201.761 197.111 1.02359
    crk-like protein. [swissprot;acc:p46109] 552 CRKL High confidence 207.26 194.346 1.06645
    1943 Low confidence 199.48 195.633 1.01966
    crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 394 CRNKL1 204.815 197.606 1.03648
    564 High confidence 220.744 207.121 1.06577
    cryptochrome 1 (photolyase-like). [refseq;acc:nm_004075] 1274 CRY1 Low confidence 193.539 189.282 1.02249
    ctcl tumor antigen l14-2. [refseq;acc:nm_018017] 2677 C10orf118 203.566 200.041 1.01762
    2846 High confidence 0.00001 0.00001 1
    ctf18, chromosome transmission fidelity factor 18 homolog; homolog of yeast chl12. [refseq;acc:nm_022092] 1619 CHTF18 Low confidence 200.714 196.617 1.02084
    ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 1755 CTPS High confidence 180.609 178.393 1.01242
    4648 Low confidence 198.39 197.136 1.00636
    cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] 1801 CUGBP1 High confidence 217.984 215.441 1.0118
    3133 Low confidence 203.381 200.103 1.01638
    cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561] 1804 CUGBP2 High confidence 217.984 215.442 1.0118
    3166 Low confidence 203.392 200.152 1.01619
    cullin homolog 1 (cul-1). [swissprot;acc:q13616] 212 CUL1 High confidence 285.684 252.234 1.13261
    625 Low confidence 203.853 198.057 1.02926
    cullin homolog 2 (cul-2). [swissprot;acc:q13617] 210 CUL2 High confidence 285.684 252.234 1.13261
    642 Low confidence 203.883 198.148 1.02894
    cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 1401 ATF2 High confidence 218.657 214.11 1.02124
    2274 Low confidence 201.301 197.582 1.01882
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 28 ATF3 High confidence 201.949 153.671 1.31416
    29 Low confidence 203.115 170.557 1.19089
    cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] 1683 ATF6 High confidence 216.899 213.889 1.01407
    1856 Low confidence 203.096 199.132 1.01991
    cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] 1680 CREBL1 High confidence 216.899 213.889 1.01407
    1853 Low confidence 203.096 199.132 1.01991
    cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 1400 ATF7 High confidence 218.667 214.118 1.02125
    2226 Low confidence 201.046 197.31 1.01893
    cyclin a1. [swissprot;acc:p78396] 614 CCNA1 187.808 182.419 1.02954
    cyclin b3 isoform 1. [refseq;acc:nm_033670] 3215 CCNB3 202.049 198.87 1.01599
    cyclin c. [swissprot;acc:p24863] 1812 CCNC High confidence 217.071 214.564 1.01168

    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/