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 description Value Type red Network Comparison Type Interaction Map Filtered network_comparison green
Results: HTML CSV LaTeX Showing element 101 to 150 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
Network Comparison Type
network_comparison
green
13 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked 266.856 Subtracted 69.377 336.233
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Squared 219048 89286 129762
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Measured 21591.5 6313 27904.5
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Ranked 288.754 Divided 1.3585 212.554
14 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 1.32952 75.3531
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] 266.863 Subtracted 69.328 336.191
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Squared 219048 89286 129762
myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Measured 21591.5 6313 27904.5
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 398.5 Divided 3.21581 1281.5
Squared 37.5863 10.3414 388.696
Rooted 19.9625 1.79326 35.798
spermatogenesis associated 6. [refseq;acc:nm_019073] 80.4705 Subtracted 21.0555 101.526
15 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
gbp protein isoform a. [refseq;acc:nm_017870] 23.9771 Divided 1.77158 42.4773
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Ranked 266.863 Subtracted 69.327 336.19
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Squared 219048 89286 129762
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Ranked 56.7244 Divided 1.32914 75.3948
myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Measured 21591.5 Subtracted 6313 27904.5
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 2671 Divided 3.06659 871
Squared 1688.58 9.40399 179.56
16 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured 24260.3 Subtracted 6088.2 18172.1
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Ranked 266.864 69.32 336.184
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 21.035 182.638
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Squared 219048 89286 129762
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Ranked 56.7252 Divided 1.32913 75.3954
protein x 0004. [refseq;acc:nm_016301] Measured 2671 3.06659 871
Squared 1688.58 9.40399 179.56
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Rooted 51.6817 1.75117 29.5127
17 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Ranked 56.7841 1.32866 75.447
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted 203.673 Subtracted 21.035 182.638
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured 460 Divided 2.96739 1365
Squared 50.0828 8.80542 441
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Ranked 266.864 Subtracted 69.318 336.182
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 24255.7 6086.8 18168.9
necdin. [swissprot;acc:q99608] Squared 219048 89286 129762
protein x 0004. [refseq;acc:nm_016301] Rooted 51.6817 Divided 1.75117 29.5127
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked 185.678 1.32082 245.247
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 203.673 Subtracted 21.035 182.638
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 21.4476 Divided 1.72261 36.9459
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 266.865 Subtracted 69.316 336.181
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared 219048 89286 129762
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured 24255.7 6086.8 18168.9
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] 677.5 Divided 2.75351 1865.5
Squared 108.641 7.58176 823.69
19 cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured 24250 Subtracted 6085.1 18164.9
cytohesin 4. [swissprot;acc:q9uia0] Rooted 203.673 21.035 182.638
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked 185.678 Divided 1.32082 245.247
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] 266.865 Subtracted 69.313 336.178
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 219048 89286 129762
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured 677.5 Divided 2.75351 1865.5

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/