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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1130 to 1179 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
565 small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] High confidence 10434.4 11846.2 1.1353
566 autoantigen ngp-1. [swissprot;acc:q13823] 3766.14 4274.79 1.13506
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Low confidence 8069.04 8442.25 1.04625
567 deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] High confidence 10264.9 9043.51 1.13506
ubiquitin-conjugating enzyme e2-32 kda complementing (ec 6.3.2.19) (ubiquitin-protein ligase) (ubiquitin carrier protein) (e2-cdc34). [swissprot;acc:p49427] Low confidence 7691.01 8046.06 1.04616
568 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] High confidence 4134.77 4691.24 1.13458
similar to cdna sequence bc023845. [sptrembl;acc:q86xc2] Low confidence 8037.33 8408.12 1.04613
569 grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] High confidence 4134.77 4691.24 1.13458
mitochondrial import inner membrane translocase subunit tim23. [swissprot;acc:o14925] Low confidence 7046.26 7370.85 1.04607
570 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] 7997.15 8364.68 1.04596
swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077] High confidence 4134.77 4691.24 1.13458
571 swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]
thimet oligopeptidase (ec 3.4.24.15) (endopeptidase 24.15) (mp78). [swissprot;acc:p52888] Low confidence 8651.4 9048.97 1.04595
572 neurolysin, mitochondrial precursor (ec 3.4.24.16) (neurotensin endopeptidase) (mitochondrial oligopeptidase m) (microsomal endopeptidase) (mep). [swissprot;acc:q9byt8]
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] High confidence 4134.77 4691.24 1.13458
573 calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] Low confidence 8506.87 8897.23 1.04589
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] High confidence 6739.43 7644.55 1.1343
574 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 6739.61 7644.58 1.13428
mouse mammary turmor virus receptor homolog 1. [refseq;acc:nm_152832] Low confidence 6869.53 7184.61 1.04587
575 14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] 8572.9 8965.49 1.04579
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] High confidence 6739.63 7644.59 1.13427
576 cg10958-like. [refseq;acc:nm_145038] Low confidence 8549.26 8940.33 1.04574
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] High confidence 6739.7 7644.6 1.13426
577 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 6739.81 7644.62 1.13425
grb2-related adaptor protein. [swissprot;acc:q13588] Low confidence 7920.96 8283.29 1.04574
578 calcyphosine. [swissprot;acc:q13938] 7873.83 8233.85 1.04572
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] High confidence 6739.81 7644.62 1.13425
579 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 6739.82
postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171] Low confidence 8683.9 9080.72 1.0457
580 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] High confidence 6739.83 7644.63 1.13425
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6] Low confidence 8569.19 8960.8 1.0457
581 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] High confidence 6739.82 7644.63 1.13425
solute carrier family 21 member 12 (sodium-independent organic anion transporter e) (organic anion transporting polypeptide e) (oatp-e) (colon organic anion transporter) (organic anion transporter polypeptide-related protein 1) (oatp-rp1) (oatprp1) (poat). [swissprot;acc:q96bd0] Low confidence 8569.19 8960.8 1.0457
582 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] High confidence 6739.82 7644.62 1.13425
histone deacetylase 4 (hd4). [swissprot;acc:p56524] Low confidence 8569.12 8960.71 1.0457
583 histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0] 8569.11 8960.7
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] High confidence 6739.81 7644.62 1.13425
584 cab2. [refseq;acc:nm_033419] Low confidence 8011.38 8377.38 1.04569
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] High confidence 6739.82 7644.63 1.13425
585 gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334]
protein hspc163. [swissprot;acc:q9p003] Low confidence 8608 9001.09 1.04567
586 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] High confidence 6739.81 7644.62 1.13425
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Low confidence 7995.61 8360.72 1.04566
587 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] High confidence 6739.83 7644.63 1.13425
588 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903]
transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] Low confidence 8611.36 9004.52 1.04566
589 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] High confidence 6739.85 7644.63 1.13424
solute carrier family 25, member 18. [swissprot;acc:q9h1k4] Low confidence 8921.54 9328.64 1.04563
590 sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 7825.64 8182.71

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/