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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 51 to 100 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
13 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Rooted 19.9625 35.798 1.79326
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Ranked 288.754 212.554 1.3585
14 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 56.6768 75.3531 1.32952
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Measured 398.5 1281.5 3.21581
Squared 37.5863 388.696 10.3414
Rooted 19.9625 35.798 1.79326
15 gbp protein isoform a. [refseq;acc:nm_017870] 23.9771 42.4773 1.77158
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Ranked 56.7244 75.3948 1.32914
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] Measured 2671 871 3.06659
Squared 1688.58 179.56 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 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
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured 460 1365 2.96739
Squared 50.0828 441 8.80542
protein x 0004. [refseq;acc:nm_016301] Rooted 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
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Rooted 21.4476 36.9459 1.72261
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Measured 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
19 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked 185.678 245.247 1.32082
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured 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 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Ranked 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Rooted 40.3337 24.2744 1.66157
protein phosphatase 1, regulatory subunit 14d; pkc-dependent pp1 inhibitory protein. [refseq;acc:nm_017726] Measured 677.5 1865.5 2.75351
Squared 108.641 823.69 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 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Rooted 40.3337 24.2744 1.66157
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Ranked 185.678 245.247 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 40.3357 24.2915 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 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
23 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Ranked 58 44 1.31818
gbp protein isoform a. [refseq;acc:nm_017870] Measured 699.76 1894.39 2.7072
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Rooted 40.3358 24.2919 1.66046
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Squared 143.692 457.521 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 40.336 24.2941 1.66032
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Ranked 58 44 1.31818
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Measured 950.561 2108.52 2.21818
25 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Squared 143.692 457.521 3.18404
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Rooted 40.3361 24.295 1.66026
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Measured 1833.01 892.67 2.0534
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Ranked 58 44 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/