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 658 to 707 of 3228 in total
    Value Type  : Ranked
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Filtered  : 1
    description
    		Rank
    		Hugo
    		red
    		network_comparison
    		green
    cullin homolog 2 (cul-2). [swissprot;acc:q13617] 210 CUL2 285.684 1.13261 252.234
    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
    cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 121 CTH 269.254 1.2169 327.655
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 14 ATG4A 56.6768 1.32952 75.3531
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 17 ATG4B 56.7841 1.32866 75.447
    cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] 1531 CRIM1 217.025 1.01744 213.304
    cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 230 CSRP1 239.35 1.11934 267.915
    cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] 1423 no value 221.152 1.02074 216.659
    cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107] 3018 CRISP1 0.00001 1 0.00001
    cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [swissprot;acc:p54108] 3150 CRISP3
    cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 1880 CDA 220.852 1.01074 223.225
    cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 1757 CTPS2 180.537 1.0124 178.325
    cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 1862 CYB5R1 210.856 1.01087 213.147
    cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 1861 CYB5R2
    cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 1511 COX11 213.268 1.01794 209.509
    cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674] 2791 COX5A 0.00001 1 0.00001
    cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854] 3009 COX6B1
    cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 2402 COX4I1 182.4 1.00374 183.083
    cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 2403 COX4I2
    cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] 1369 HCCS 228.644 1.02194 223.736
    cytochrome c. [swissprot;acc:p00001] 1533 CYCS 228.419 1.01732 232.376
    cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 501 CYC1 238.704 1.07112 255.68
    cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] 1332 OXA1L 220.681 1.02271 215.78
    cytochrome p450 24a1, mitochondrial precursor (ec 1.14.-.-) (p450- cc24) (vitamin d(3) 24-hydroxylase) (1,25-dihydroxyvitamin d(3) 24- hydroxylase) (24-ohase). [swissprot;acc:q07973] 3211 CYP24A1 0.00001 1 0.00001
    cytochrome p450 27, mitochondrial precursor (ec 1.14.-.-) (cytochrome p-450c27/25) (sterol 26-hydroxylase) (sterol 27-hydroxylase) (vitamin d(3) 25-hydroxylase) (5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase). [swissprot;acc:q02318] 2977 CYP27A1
    cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635] 1258 CYP2D6 219.354 1.02437 224.7
    cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] 1280 CYP4A11 218.368 1.02414 213.22
    cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] 1288 CYP4B1

    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/