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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Gene Rank Network Comparison Type description Value Type green Filtered network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 151 to 200 of 25824 in total
Filtered  : 1
Interaction Map  : High confidence
Rank
Network Comparison Type
description
Value Type
green
network_comparison
red
19 Subtracted guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked 336.178 69.313 266.865
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 129762 89286 219048
20 Divided glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Ranked 245.247 1.32082 185.678
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Rooted 24.2744 1.66157 40.3337
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured 1865.5 2.75351 677.5
Squared 823.69 7.58176 108.641
Subtracted cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Rooted 182.638 21.035 203.673
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Measured 17580.4 5841.1 23421.5
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 336.159 69.291 266.868
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared 129762 89286 219048
21 Divided ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] Measured 1865.5 2.75351 677.5
Squared 823.69 7.58176 108.641
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Rooted 24.2744 1.66157 40.3337
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 245.247 1.32082 185.678
Subtracted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Rooted 133.195 20.407 153.602
gbp protein isoform a. [refseq;acc:nm_017870] Ranked 256.492 69.094 325.586
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Measured 18263 5430.7 23693.7
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared 129762 89286 219048
22 Divided glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Ranked 245.247 1.32082 185.678
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Rooted 24.2915 1.66049 40.3357
protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949] Measured 1865.5 2.75351 677.5
Squared 823.69 7.58176 108.641
Subtracted hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Measured 18263 5430.7 23693.7
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Squared 129762 89286 219048
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Rooted 133.176 20.402 153.578
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Ranked 253 69 322
23 Divided 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 44 1.31818 58
gbp protein isoform a. [refseq;acc:nm_017870] Measured 1894.39 2.7072 699.76
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Rooted 24.2919 1.66046 40.3358
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Squared 457.521 3.18404 143.692
Subtracted melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Measured 18263 5430.7 23693.7
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared 129762 89286 219048
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Ranked 253 69 322
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Rooted 133.176 20.402 153.578
24 Divided chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Squared 457.521 3.18404 143.692
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Rooted 24.2941 1.66032 40.336
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Ranked 44 1.31818 58
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured 2108.52 2.21818 950.561
Subtracted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Rooted 133.153 20.395 153.548
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Measured 18263 5430.7 23693.7
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 129762 89286 219048
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Ranked 253 69 322
25 Divided doc-1 related protein (doc-1r). [swissprot;acc:o75956] Squared 457.521 3.18404 143.692
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Rooted 24.295 1.66026 40.3361
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Measured 892.67 2.0534 1833.01
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Ranked 44 1.31818 58
Subtracted ficolin 2 precursor (collagen/fibrinogen domain-containing protein 2) (ficolin-b) (ficolin b) (serum lectin p35) (ebp-37) (hucolin) (l- ficolin). [swissprot;acc:q15485] 253 69 322
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 129762 89286 219048
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Measured 18263 5430.7 23693.7
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Rooted 167.046 20.106 146.94

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/