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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Network Comparison Type Rank Gene description Value Type Interaction Map red Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 101 to 150 of 16578 in total
Network Comparison Type  : Divided
Value Type  : Measured
Filtered  : 1
Rank
description
Interaction Map
red
network_comparison
green
51 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Low confidence 7563.09 1.15458 8732.2
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence 779.167 1.78438 1390.33
52 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Low confidence 13195.9 1.14883 11486.4
53 bcl2-related ovarian killer. [refseq;acc:nm_032515] 4955.33 1.14207 5659.35
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] High confidence 779.167 1.78438 1390.33
54 deltex 2. [refseq;acc:nm_020892] 1618.84 1.63814 2651.88
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence 13203.5 1.13859 15033.4
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] High confidence 1629.21 1.63399 2662.12
septin 10 isoform 1. [refseq;acc:nm_144710] Low confidence 13081.2 1.13694 14872.6
56 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 15464.1 1.13635 17572.7
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] High confidence 1631.67 1.63302 2664.55
57 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 15464.1 1.13635 17572.7
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 1631.67 1.63302 2664.55
58 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence 15464.1 1.13635 17572.7
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 1631.67 1.63302 2664.55
59 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 15464.1 1.13635 17572.7
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence 1631.67 1.63302 2664.55
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 1.6231 2765.82
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 15464.1 1.13635 17572.7
61 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 4489.19 1.6231 2765.82
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Low confidence 15464.1 1.13635 17572.7
62 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 4489.19 1.6231 2765.82
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 15464.1 1.13635 17572.7
63 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] High confidence 4489.19 1.6231 2765.82
64 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence 15464.1 1.13635 17572.7
65 neuralized-like. [refseq;acc:nm_004210] High confidence 1657.68 1.6229 2690.25
septin 6. [swissprot;acc:q14141] Low confidence 13005.8 1.13593 14773.7
66 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] High confidence 1991.03 1.61795 3221.38
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] Low confidence 4900.7 1.13368 5555.81
67 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] High confidence 6475.5 1.59177 10307.5
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Low confidence 12176.9 1.1318 13781.8
68 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] High confidence 6475.5 1.59177 10307.5
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Low confidence 19498.1 1.12932 17265.4
69 amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817] 6991.78 1.12253 7848.45
spermatogenesis associated 6. [refseq;acc:nm_019073] High confidence 6475.5 1.59177 10307.5
70 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
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] Low confidence 6991.78 1.12253 7848.45
71 cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5]
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] High confidence 4556.78 1.54716 2945.26
72 solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Low confidence 6991.78 1.12253 7848.45
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] High confidence 4556.79 1.54715 2945.28
73 eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Low confidence 6991.78 1.12253 7848.45
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] High confidence 4556.83 1.54711 2945.38
74 b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] Low confidence 6991.78 1.12253 7848.45
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] High confidence 4556.99 1.54694 2945.8
75 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 1.5137 2907.43
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Low confidence 11616 1.11418 12942.3

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/