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 Value Type description green Interaction Map red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Value Type
description
green
red
network_comparison
13 Subtracted Measured myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 27904.5 21591.5 6313
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 336.233 266.856 69.377
Squared melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 129762 219048 89286
Rooted beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 101.526 80.4705 21.0555
14 Divided Measured ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 1281.5 398.5 3.21581
Ranked cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 75.3531 56.6768 1.32952
Squared ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 388.696 37.5863 10.3414
Rooted 35.798 19.9625 1.79326
Subtracted Measured myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 27904.5 21591.5 6313
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 336.191 266.863 69.328
Squared melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 129762 219048 89286
Rooted spermatogenesis associated 6. [refseq;acc:nm_019073] 101.526 80.4705 21.0555
15 Divided Measured xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 871 2671 3.06659
Ranked microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 75.3948 56.7244 1.32914
Squared xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 179.56 1688.58 9.40399
Rooted gbp protein isoform a. [refseq;acc:nm_017870] 42.4773 23.9771 1.77158
Subtracted Measured myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 27904.5 21591.5 6313
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] 336.19 266.863 69.327
Squared hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 129762 219048 89286
Rooted amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 101.526 80.4705 21.0555
16 Divided Measured protein x 0004. [refseq;acc:nm_016301] 871 2671 3.06659
Ranked microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 75.3954 56.7252 1.32913
Squared protein x 0004. [refseq;acc:nm_016301] 179.56 1688.58 9.40399
Rooted xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 29.5127 51.6817 1.75117
Subtracted Measured cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 18172.1 24260.3 6088.2
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] 336.184 266.864 69.32
Squared melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 129762 219048 89286
Rooted 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] 182.638 203.673 21.035
17 Divided Measured dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 1365 460 2.96739
Ranked cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 75.447 56.7841 1.32866
Squared dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 441 50.0828 8.80542
Rooted protein x 0004. [refseq;acc:nm_016301] 29.5127 51.6817 1.75117
Subtracted Measured microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 18168.9 24255.7 6086.8
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] 336.182 266.864 69.318
Squared necdin. [swissprot;acc:q99608] 129762 219048 89286
Rooted cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 182.638 203.673 21.035
18 Divided Measured protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 1865.5 677.5 2.75351
Ranked 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 245.247 185.678 1.32082
Squared protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 823.69 108.641 7.58176
Rooted dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 36.9459 21.4476 1.72261
Subtracted Measured microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 18168.9 24255.7 6086.8
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 336.181 266.865 69.316
Squared melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 129762 219048 89286
Rooted cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 182.638 203.673 21.035
19 Divided Measured microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 1865.5 677.5 2.75351
Ranked glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 245.247 185.678 1.32082
Squared microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] 823.69 108.641 7.58176
Rooted protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 43.561 25.6987 1.69507
Subtracted Measured cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 18164.9 24250 6085.1
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 336.178 266.865 69.313

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/