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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 80 to 129 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
40 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] High confidence 1836.81 907.978 2.02297
41 guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Low confidence 6481.62 7600.61 1.17264
42 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 6485.05 7601.81 1.17221
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] High confidence 1857.32 958.237 1.93827
43 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Low confidence 13689.1 11788.6 1.16122
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] High confidence 1881.02 1027.36 1.83093
44 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 1931.34 1057.39 1.82652
transcription factor jun-d. [swissprot;acc:p17535] Low confidence 6614.51 7680.25 1.16112
45 guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] High confidence 1926.69 1056.02 1.82448
transcription factor jun-b. [swissprot;acc:p17275] Low confidence 6613.42 7678.76 1.16109
46 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] High confidence 779.167 1390.33 1.78438
transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867] Low confidence 8313.02 9645.34 1.16027
47 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] High confidence 779.167 1390.33 1.78438
nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236] Low confidence 8313.02 9645.34 1.16027
48 doc-1 related protein (doc-1r). [swissprot;acc:o75956] High confidence 779.167 1390.33 1.78438
transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9] Low confidence 8313.02 9645.34 1.16027
49 microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 13470.1 11654.4 1.1558
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 779.167 1390.33 1.78438
50 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Low confidence 13466.8 11652.4 1.15571
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] High confidence 779.167 1390.33 1.78438
51 dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Low confidence 7563.09 8732.2 1.15458
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] High confidence 779.167 1390.33 1.78438
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 11486.4 1.14883
53 bcl2-related ovarian killer. [refseq;acc:nm_032515] 4955.33 5659.35 1.14207
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 1390.33 1.78438
54 deltex 2. [refseq;acc:nm_020892] 1618.84 2651.88 1.63814
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence 13203.5 15033.4 1.13859
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] High confidence 1629.21 2662.12 1.63399
septin 10 isoform 1. [refseq;acc:nm_144710] Low confidence 13081.2 14872.6 1.13694
56 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 15464.1 17572.7 1.13635
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 2664.55 1.63302
57 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 15464.1 17572.7 1.13635
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 1631.67 2664.55 1.63302
58 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Low confidence 15464.1 17572.7 1.13635
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 1631.67 2664.55 1.63302
59 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 15464.1 17572.7 1.13635
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence 1631.67 2664.55 1.63302
60 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
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 15464.1 17572.7 1.13635
61 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] High confidence 4489.19 2765.82 1.6231
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Low confidence 15464.1 17572.7 1.13635
62 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] High confidence 4489.19 2765.82 1.6231
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 15464.1 17572.7 1.13635
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 2765.82 1.6231
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 17572.7 1.13635
65 neuralized-like. [refseq;acc:nm_004210] High confidence 1657.68 2690.25 1.6229

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/