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 632 to 681 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363] 3168 TMED2 0.00001 1 0.00001
    cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] 1500 COPS4 213.398 1.01851 209.52
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 175 COPS3 199.949 1.17123 234.187
    cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837] 2380 COPS5 212.724 1.004 213.574
    cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] 2827 GPS1 0.00001 1 0.00001
    cop9 signalosome complex subunit 2 (signalosome subunit 2) (sgn2) (thyroid receptor interacting protein 15) (trip15). [swissprot;acc:q15647] 2841 COPS2
    cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833] 2374 COPS6 212.724 1.004 213.574
    copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] 2352 ATP7A 215.088 1.00436 214.155
    copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] 2354 ATP7B 215.078 1.00434 214.148
    coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551] 2617 CPOX 202.821 1.00139 202.54
    core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [swissprot;acc:q13951] 3183 CBFB 0.00001 1 0.00001
    cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] 1513 COX15 213.268 1.01794 209.509
    cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] 1168 CXXC1 219.399 1.02626 213.784
    cpz gene product. [refseq;acc:nm_003652] 716 CPZ 223.121 1.05402 211.685
    creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] 1940 CKB 198.19 1.00988 196.252
    creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] 1971 CKM 198.258 1.00974 196.346
    creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] 1936 CKMT2 198.3 1.00995 196.347
    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 198.293 1.00994 196.341
    crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 284 BCAR1 224.657 1.10541 203.235
    crk-like protein. [swissprot;acc:p46109] 552 CRKL 207.26 1.06645 194.346
    crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 564 CRNKL1 220.744 1.06577 207.121
    ctcl tumor antigen l14-2. [refseq;acc:nm_018017] 2846 C10orf118 0.00001 1 0.00001
    ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 1755 CTPS 180.609 1.01242 178.393
    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 217.984 1.0118 215.441
    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 215.442
    cullin homolog 1 (cul-1). [swissprot;acc:q13616] 212 CUL1 285.684 1.13261 252.234
    cullin homolog 2 (cul-2). [swissprot;acc:q13617] 210 CUL2
    cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 1401 ATF2 218.657 1.02124 214.11
    cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 28 ATF3 201.949 1.31416 153.671
    cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] 1683 ATF6 216.899 1.01407 213.889
    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
    cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 1400 ATF7 218.667 1.02125 214.118
    cyclin c. [swissprot;acc:p24863] 1812 CCNC 217.071 1.01168 214.564
    cyclin g1 (cyclin g). [swissprot;acc:p51959] 963 CCNG1 130.066 1.0343 134.527
    cyclin g2. [swissprot;acc:q16589] 962 CCNG2
    cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 2983 CCNH 0.00001 1 0.00001
    cyclin k. [swissprot;acc:o75909] 3160 CCNK
    cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] 2606 CNNM1 214.5 1.00141 214.198
    cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] 2604 CNNM2 214.486 214.184
    cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] 2601 CNNM3 214.502 214.2
    cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] 2603 CNNM4 214.494 214.192
    cyclin t1 (cyclin t) (cyct1). [swissprot;acc:o60563] 3002 CCNT1 0.00001 1 0.00001
    cyclin t2. [swissprot;acc:o60583] 3171 CCNT2
    cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [refseq;acc:nm_015076] 2892 CDC2L6
    cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 336 CDK2AP1 312 1.09859 284
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 1452 no value 160.381 1.01978 163.554
    cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 1833 CKS2 180.409 1.01136 182.459
    cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] 2570 CYLD 219.907 1.00164 220.267
    cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [swissprot;acc:o00622] 2938 CYR61 0.00001 1 0.00001
    cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 1022 CBS 205.632 1.03195 199.266

    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/