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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Network Comparison Type Gene Rank description Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 25824 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
green
red
network_comparison
13 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted 35.798 19.9625 1.79326
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Ranked 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
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Measured 1281.5 398.5 3.21581
Squared 388.696 37.5863 10.3414
Rooted 35.798 19.9625 1.79326
15 gbp protein isoform a. [refseq;acc:nm_017870] 42.4773 23.9771 1.77158
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Ranked 75.3948 56.7244 1.32914
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Measured 871 2671 3.06659
Squared 179.56 1688.58 9.40399
16 microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Ranked 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
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured 1365 460 2.96739
Squared 441 50.0828 8.80542
protein x 0004. [refseq;acc:nm_016301] Rooted 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
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Rooted 36.9459 21.4476 1.72261
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Measured 1865.5 677.5 2.75351
Squared 823.69 108.641 7.58176
19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked 245.247 185.678 1.32082
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured 1865.5 677.5 2.75351
Squared 823.69 108.641 7.58176
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Rooted 43.561 25.6987 1.69507
20 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Ranked 245.247 185.678 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Rooted 24.2744 40.3337 1.66157
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured 1865.5 677.5 2.75351
Squared 823.69 108.641 7.58176
21 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 1865.5 677.5 2.75351
Squared 823.69 108.641 7.58176
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Rooted 24.2744 40.3337 1.66157
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 245.247 185.678 1.32082
22 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Rooted 24.2915 40.3357 1.66049
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 1865.5 677.5 2.75351
Squared 823.69 108.641 7.58176
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Ranked 44 58 1.31818
gbp protein isoform a. [refseq;acc:nm_017870] Measured 1894.39 699.76 2.7072
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Rooted 24.2919 40.3358 1.66046
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Squared 457.521 143.692 3.18404
24 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Rooted 24.2941 40.336 1.66032
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Ranked 44 58 1.31818
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured 2108.52 950.561 2.21818
25 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Squared 457.521 143.692 3.18404
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Rooted 24.295 40.3361 1.66026
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Measured 892.67 1833.01 2.0534
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Ranked 44 58 1.31818

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/