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 118 to 167 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
15 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Measured Subtracted 21591.5 27904.5 6313
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Divided 2671 871 3.06659
Squared 1688.58 179.56 9.40399
16 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured Subtracted 24260.3 18172.1 6088.2
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked 266.864 336.184 69.32
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Rooted 203.673 182.638 21.035
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 219048 129762 89286
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Ranked Divided 56.7252 75.3954 1.32913
protein x 0004. [refseq;acc:nm_016301] Measured 2671 871 3.06659
Squared 1688.58 179.56 9.40399
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Rooted 51.6817 29.5127 1.75117
17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Ranked 56.7841 75.447 1.32866
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted Subtracted 203.673 182.638 21.035
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured Divided 460 1365 2.96739
Squared 50.0828 441 8.80542
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked Subtracted 266.864 336.182 69.318
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 24255.7 18168.9 6086.8
necdin. [swissprot;acc:q99608] Squared 219048 129762 89286
protein x 0004. [refseq;acc:nm_016301] Rooted Divided 51.6817 29.5127 1.75117
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked 185.678 245.247 1.32082
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted Subtracted 203.673 182.638 21.035
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Divided 21.4476 36.9459 1.72261
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked Subtracted 266.865 336.181 69.316
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared 219048 129762 89286
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured 24255.7 18168.9 6086.8
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
19 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured Subtracted 24250 18164.9 6085.1
cytohesin 4. [swissprot;acc:q9uia0] Rooted 203.673 182.638 21.035
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked Divided 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 266.865 336.178 69.313
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 219048 129762 89286
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Rooted 25.6987 43.561 1.69507
20 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Subtracted 203.673 182.638 21.035
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Measured 23421.5 17580.4 5841.1
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Ranked Divided 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Subtracted 266.868 336.159 69.291
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Rooted Divided 40.3337 24.2744 1.66157
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared Subtracted 219048 129762 89286
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
21 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Rooted Subtracted 153.602 133.195 20.407
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 Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
gbp protein isoform a. [refseq;acc:nm_017870] Ranked Subtracted 325.586 256.492 69.094
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Rooted Divided 40.3337 24.2744 1.66157
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Measured Subtracted 23693.7 18263 5430.7
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared 219048 129762 89286

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/