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 1675 to 1724 of 8289 in total
    Network Comparison Type  : Divided
    Value Type  : Ranked
    Filtered  : 1
    description
    		Rank
    		Hugo
    		Interaction Map
    		red
    		green
    		network_comparison
    cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] 2601 CNNM3 High confidence 214.502 214.2 1.00141
    cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] 2027 CNNM4 Low confidence 199.277 195.483 1.01941
    2603 High confidence 214.494 214.192 1.00141
    cyclin t1 (cyclin t) (cyct1). [swissprot;acc:o60563] 2619 CCNT1 Low confidence 202.506 206.117 1.01783
    3002 High confidence 0.00001 0.00001 1
    cyclin t2. [swissprot;acc:o60583] 2616 CCNT2 Low confidence 202.507 206.119 1.01784
    3171 High confidence 0.00001 0.00001 1
    cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [refseq;acc:nm_015076] 2892 CDC2L6
    4249 Low confidence 202.892 204.84 1.0096
    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 High confidence 312 284 1.09859
    694 Low confidence 216.501 210.602 1.02801
    cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 1452 no value High confidence 160.381 163.554 1.01978
    1707 Low confidence 201.609 197.553 1.02053
    cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 1753 CKS2 202.553 198.516 1.02034
    1833 High confidence 180.409 182.459 1.01136
    cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] 2570 CYLD 219.907 220.267 1.00164
    4676 Low confidence 182.189 181.112 1.00595
    cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [swissprot;acc:o00622] 1405 CYR61 208.227 203.771 1.02187
    2938 High confidence 0.00001 0.00001 1
    cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 1022 CBS 205.632 199.266 1.03195
    1650 Low confidence 199.148 195.11 1.0207
    cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 121 CTH High confidence 269.254 327.655 1.2169
    1508 Low confidence 203.663 199.402 1.02137
    cysteine and histidine-rich domain (chord)-containing, zinc binding protein 1; chord domain-containing protein 1; cysteine and histidine-rich domain (chord)-containing, zinc-binding protein 1. [refseq;acc:nm_012124] 1592 CHORDC1 206.658 202.403 1.02102
    cysteine endopeptidase aut-like 1; autophagin-3. [refseq;acc:nm_032852] 3376 ATG4C 197.702 194.704 1.0154
    cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 14 ATG4A High confidence 56.6768 75.3531 1.32952
    985 Low confidence 151.012 154.728 1.02461
    cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 17 ATG4B High confidence 56.7841 75.447 1.32866
    2119 Low confidence 155.486 158.471 1.0192
    cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] 1531 CRIM1 High confidence 217.025 213.304 1.01744
    2676 Low confidence 204.508 200.964 1.01763
    cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 230 CSRP1 High confidence 239.35 267.915 1.11934
    4611 Low confidence 208.115 209.563 1.00696
    cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] 71 no value 230.944 209.149 1.10421
    1423 High confidence 221.152 216.659 1.02074
    cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107] 2689 CRISP1 Low confidence 205.763 202.207 1.01759
    3018 High confidence 0.00001 0.00001 1
    cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [swissprot;acc:p54108] 2990 CRISP3 Low confidence 204.374 201.005 1.01676
    3150 High confidence 0.00001 0.00001 1
    cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] 97 SLC7A11 Low confidence 200.497 185.679 1.0798
    cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 1880 CDA High confidence 220.852 223.225 1.01074
    3252 Low confidence 200.267 197.148 1.01582
    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 High confidence 180.537 178.325 1.0124
    4631 Low confidence 198.337 197.028 1.00664
    cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] 252 CYBB 210.414 201.035 1.04665
    cytochrome b5 outer mitochondrial membrane isoform precursor. [swissprot;acc:o43169] 3614 CYB5B 201.988 199.144 1.01428
    cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 1335 CYB5R1 200.614 196.269 1.02214
    1862 High confidence 210.856 213.147 1.01087
    cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 1113 CYB5R2 Low confidence 200.326 195.686 1.02371
    1861 High confidence 210.856 213.147 1.01087

    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/