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 [...,...].
    Value Type Filtered Rank description Gene Network Comparison Type Interaction Map green red network_comparison
    Results: HTML CSV LaTeX Showing element 451 to 500 of 3730 in total
    Value Type  : Ranked
    Filtered  : 0
    Network Comparison Type  : Divided
    Interaction Map  : High confidence
    Rank
    description
    green
    red
    network_comparison
    451 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] 13737.2 14010.2 1.01987
    452 neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]
    453 transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]
    454 lats homolog 1. [refseq;acc:nm_004690] 14204.8 13933.5 1.01947
    455 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
    456 williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] 16721.6 16416.1 1.01861
    457 williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]
    458 williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
    459 translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] 20495 20875 1.01854
    460 mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932] 20558 20914 1.01732
    461 scratch; scratch 1. [refseq;acc:nm_031309] 12358.1 12164.9 1.01588
    462 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 12378.3 12189.6 1.01548
    463 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 5473.99 5558.06 1.01536
    464 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 9928.08 10076.4 1.01494
    465 transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 9620.66 9482.68 1.01455
    466 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 1521 1543 1.01446
    467 histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261] 20914 21205 1.01391
    468 histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
    469 histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
    470 h2a histone family, member j isoform 1. [refseq;acc:nm_018267]
    471 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 11463 11319.2 1.0127
    472 peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] 7165.6 7080.27 1.01205
    473 cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] 825 816 1.01103
    474 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] 11167.6 11290.1 1.01097
    475 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 18500 18667 1.00903
    476 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 8329 8403 1.00888
    477 ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 15780.2 15920 1.00886
    478 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 10243.1 10156.4 1.00854
    479 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] 15031.7 15155.8 1.00826
    480 uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]
    481 uridine kinase-like 1. [swissprot;acc:q9nwz5] 11462.4 11554.3 1.00802
    482 kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] 6205.67 6156.33 1.00801
    483 tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 12127.5 12223.8 1.00794
    484 protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] 11414.3 11489.7 1.00661
    485 pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 12542.3 12461.5 1.00648
    486 huntingtin interacting protein c. [refseq;acc:nm_012272] 13288.3 13372.4 1.00633
    487 survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] 13159.3 13236.8 1.00589
    488 heat shock factor binding protein 1. [swissprot;acc:o75506] 15127.8 15204.2 1.00505
    489 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 8811.09 8854.04 1.00487
    490 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 10338.7 10388.7 1.00484
    491 rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] 21880 21970 1.00411
    492 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 6829.74 6802.96 1.00394
    493 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 12041.7 11999.1 1.00355
    494 signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 11959.4 11985.5 1.00218
    495 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 11748.1 11725.2 1.00195
    496 vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] 9411.49 9394 1.00186
    497 sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 13718.2 13692.7
    498 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 10248.3 10231.8 1.00161
    499 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 9069.58 9080.73 1.00123
    500 huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 394 394 1

    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
    - 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/