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

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/