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 130 to 179 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
33 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Divided 0 12.6208 39.8063 3.15402
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Subtracted 1 23693.7 18263 5430.7
protein cgi-147. [swissprot;acc:q9y3e5] 0 8396.12 9192.38 796.26
34 acrc protein; putative nuclear protein. [refseq;acc:nm_052957] 4131.06 3340.03 791.03
glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] Divided 143 47 3.04255
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 1 1836.71 907.546 2.02382
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Subtracted 23693.7 18263 5430.7
35 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Divided 0 459.5 1377 2.99674
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Subtracted 1603 898 705
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Divided 1 1836.71 907.564 2.02378
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Subtracted 23693.7 18263 5430.7
36 guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Divided 1836.76 907.741 2.02344
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 0 157 56 2.80357
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Subtracted 1 23693.7 18263 5430.7
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 0 1586.07 925.298 660.772
37 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Divided 334.401 934.348 2.79409
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 1 1836.76 907.763 2.02339
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Subtracted 23693.7 18263 5430.7
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] 0 5202.89 4550.64 652.25
38 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] 5497.01 6127.24 630.23
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Divided 1 1836.76 907.774 2.02337
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Subtracted 23693.7 18263 5430.7
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Divided 0 320.012 120.429 2.65727
39 guanine nucleotide-binding protein g(i), alpha-2 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04899] 1 1836.8 907.903 2.02312
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Subtracted 23693.7 18263 5430.7
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Divided 0 482.426 192.295 2.50878
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Subtracted 973.698 1601.52 627.822
40 guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Divided 1 1836.81 907.978 2.02297
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] Subtracted 23693.7 18263 5430.7
nanos (fragment). [sptrembl;acc:q8wy41] Divided 0 377 151 2.49669
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Subtracted 148 773 625
41 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 6131.07 6739.34 608.27
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Divided 1 1836.81 907.978 2.02297
nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718] 0 266 645 2.42481
trophinin. [swissprot;acc:q12816] Subtracted 1 23693.7 18263 5430.7
42 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 21785.2 16426.1 5359.1
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Divided 1857.32 958.237 1.93827
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 0 205.439 86.9525 2.36266
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 18889 19496 607
43 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 1 21785.2 16426.1 5359.1
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Divided 0 263.66 587.988 2.2301
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 1 1881.02 1027.36 1.83093
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Subtracted 0 4089.65 4696.36 606.71
44 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Divided 45.4292 98.5074 2.16837
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Subtracted 1 28136.5 33457.6 5321.1
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Divided 1931.34 1057.39 1.82652
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Subtracted 0 2285.62 1681.3 604.32
45 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 334.401 934.348 599.947
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Divided 1 1926.69 1056.02 1.82448
protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Subtracted 27642.5 22440.4 5202.1

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/