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 Interaction Map description Network Comparison Type red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
Interaction Map
description
red
green
network_comparison
51 High confidence neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 779.167 1390.33 1.78438
Low confidence dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] 7563.09 8732.2 1.15458
52 High confidence chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 779.167 1390.33 1.78438
Low confidence cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 13195.9 11486.4 1.14883
53 High confidence 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] 779.167 1390.33 1.78438
Low confidence bcl2-related ovarian killer. [refseq;acc:nm_032515] 4955.33 5659.35 1.14207
54 High confidence deltex 2. [refseq;acc:nm_020892] 1618.84 2651.88 1.63814
Low confidence septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 13203.5 15033.4 1.13859
55 High confidence deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 1629.21 2662.12 1.63399
Low confidence septin 10 isoform 1. [refseq;acc:nm_144710] 13081.2 14872.6 1.13694
56 High confidence t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] 1631.67 2664.55 1.63302
Low confidence homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 15464.1 17572.7 1.13635
57 High confidence kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1631.67 2664.55 1.63302
Low confidence homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 15464.1 17572.7 1.13635
58 High confidence kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1631.67 2664.55 1.63302
Low confidence homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 15464.1 17572.7 1.13635
59 High confidence kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 1631.67 2664.55 1.63302
Low confidence homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 15464.1 17572.7 1.13635
60 High confidence 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 2765.82 1.6231
Low confidence homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 15464.1 17572.7 1.13635
61 High confidence glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 4489.19 2765.82 1.6231
Low confidence homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 15464.1 17572.7 1.13635
62 High confidence glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 4489.19 2765.82 1.6231
Low confidence homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 15464.1 17572.7 1.13635
63 High confidence myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 4489.19 2765.82 1.6231
Low confidence homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 15464.1 17572.7 1.13635
64 High confidence glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 4489.19 2765.82 1.6231
Low confidence retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 15464.1 17572.7 1.13635
65 High confidence neuralized-like. [refseq;acc:nm_004210] 1657.68 2690.25 1.6229
Low confidence septin 6. [swissprot;acc:q14141] 13005.8 14773.7 1.13593
66 High confidence nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 1991.03 3221.38 1.61795
Low confidence son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] 4900.7 5555.81 1.13368
67 High confidence beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 6475.5 10307.5 1.59177
Low confidence hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 12176.9 13781.8 1.1318
68 High confidence beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 6475.5 10307.5 1.59177
Low confidence putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 19498.1 17265.4 1.12932
69 High confidence spermatogenesis associated 6. [refseq;acc:nm_019073] 6475.5 10307.5 1.59177
Low confidence amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] 6991.78 7848.45 1.12253
70 High confidence amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 6475.5 10307.5 1.59177
Low confidence y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] 6991.78 7848.45 1.12253
71 High confidence serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 4556.78 2945.26 1.54716
Low confidence cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] 6991.78 7848.45 1.12253
72 High confidence uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 4556.79 2945.28 1.54715
Low confidence solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] 6991.78 7848.45 1.12253
73 High confidence serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 4556.83 2945.38 1.54711
Low confidence eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] 6991.78 7848.45 1.12253
74 High confidence serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 4556.99 2945.8 1.54694
Low confidence b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] 6991.78 7848.45 1.12253
75 High confidence nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] 1920.75 2907.43 1.5137
Low confidence septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 11616 12942.3 1.11418

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/