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 red green network_comparison
Results: HTML CSV LaTeX Showing element 250 to 299 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
16 phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Squared Divided 0 0.00001 0.0766864 7668.64
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] Measured 1 15 15
protein x 0004. [refseq;acc:nm_016301] 1 2671 871 3.06659
Squared 1688.58 179.56 9.40399
ptd016 protein. [refseq;acc:nm_016125] Ranked Subtracted 0 18050 11234 6816
serpin b12. [swissprot;acc:q96p63] Rooted Divided 10.2928 1.18697 8.67149
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 51.6817 29.5127 1.75117
17 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Measured Subtracted 0 11223 12473 1250
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Squared 25050 42114.6 17064.6
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Ranked Divided 1 56.7841 75.447 1.32866
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] Rooted Subtracted 203.673 182.638 21.035
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Measured Divided 460 1365 2.96739
Squared 50.0828 441 8.80542
ero1-like. [refseq;acc:nm_014584] Ranked Subtracted 0 13853 20536 6683
fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Divided 11543 6812 1.69451
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Subtracted 1 266.864 336.182 69.318
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Rooted Divided 0 10.3085 1.2188 8.45791
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured Subtracted 1 24255.7 18168.9 6086.8
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 0 859 58 14.8103
necdin. [swissprot;acc:q99608] Squared Subtracted 1 219048 129762 89286
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Rooted 0 12.4097 0 12.4097
protein x 0004. [refseq;acc:nm_016301] Divided 1 51.6817 29.5127 1.75117
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] Squared 0 0.0766864 0.00001 7668.64
18 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Ranked 1 185.678 245.247 1.32082
60s ribosomal protein l37a. [swissprot;acc:p12751] Measured 0 305.45 26.1599 11.6763
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Squared 439.709 0.52284 841.001
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Measured Subtracted 15411.3 14167 1244.3
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Rooted Divided 9.20014 60.0707 6.52932
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Squared Subtracted 43393.5 56658.6 13265.1
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] Rooted 1 203.673 182.638 21.035
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Divided 21.4476 36.9459 1.72261
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Ranked Subtracted 0 7509.39 14178.1 6668.71
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] 1 266.865 336.181 69.316
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 0 22286 13216 1.68629
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared Subtracted 1 219048 129762 89286
microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Measured 24255.7 18168.9 6086.8
protein phosphatase 1, regulatory (inhibitor) subunit 14a; 17-kda pkc-potentiated inhibitory protein of pp1. [refseq;acc:nm_033256] Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Rooted Subtracted 0 12.4097 0 12.4097
19 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Measured Divided 305.45 26.1599 11.6763
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Subtracted 1 24250 18164.9 6085.1
cytohesin 4. [swissprot;acc:q9uia0] Rooted 203.673 182.638 21.035
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Measured 0 1593 2804 1211
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked Divided 1 185.678 245.247 1.32082
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Subtracted 266.865 336.178 69.313
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 0 22286 13216 1.68629
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Rooted 9.20014 60.0707 6.52932
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared Subtracted 1 219048 129762 89286
microfibril-associated glycoprotein 4 precursor. [swissprot;acc:p55083] Measured Divided 677.5 1865.5 2.75351
Squared 108.641 823.69 7.58176

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/