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 951 to 1000 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
119 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 0 4.72248 5.90479 1.25036
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 1 50.3247 62.9892 1.25166
120 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 0 22.9115 28.547 1.24597
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Measured 1 5136.78 6895.98 1.34247
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Rooted 50.3333 62.9942 1.25154
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Squared 210199 136638 1.53836
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked 269.278 327.709 1.21699
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 0 5797 4873 1.18962
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Measured 494.417 359.631 1.37479
syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623] Squared 6.45653 12.2937 1.90407
121 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] Measured 19.6667 14.3333 1.3721
alpha crystallin a chain. [swissprot;acc:p02489] Squared 1.27019 2.40686 1.89488
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Ranked 1 269.254 327.655 1.2169
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Rooted 50.339 62.9975 1.25147
myosin vi. [swissprot;acc:q9um54] 0 17.3551 14.0846 1.2322
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Squared 1 199594 130021 1.53509
transcription factor jun-b. [swissprot;acc:p17275] Measured 5579.18 7488.4 1.3422
zinc finger protein 232. [swissprot;acc:q9uny5] Ranked 0 11523.7 13686.9 1.18772
122 cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared 1 201896 131906 1.53061
high-mobility group 20a. [refseq;acc:nm_018200] Measured 5140.14 6893.53 1.34112
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] Rooted 0 9.00325 7.33715 1.22708
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Ranked 1 269.248 327.642 1.21688
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] Measured 0 107 78 1.37179
transcription factor jun-d. [swissprot;acc:p17535] Rooted 1 63.636 79.6225 1.25122
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] Squared 0 34.1583 18.0543 1.89198
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Ranked 11523 13685.4 1.18766
123 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Measured 1 24260.3 18172.1 1.33503
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Rooted 54.6527 67.9743 1.24375
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Ranked 269.23 327.601 1.21681
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Rooted 0 27.4843 22.4483 1.22434
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 1 192904 126167 1.52896
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] Measured 0 2285.62 1681.3 1.35944
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Squared 31.8185 16.8625 1.88694
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Ranked 11522.8 13684.9 1.18764
124 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Rooted 10.6611 13.034 1.22258
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Ranked 1 208.52 171.595 1.21519
microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Measured 24255.7 18168.9 1.33501
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Rooted 54.6625 67.9477 1.24304
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Measured 0 3248.95 2399.76 1.35386
sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [refseq;acc:nm_015503] Squared 2.70982 1.44 1.88182
type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 1 192779 126095 1.52884
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Ranked 0 11520.7 13680.4 1.18746
125 high-mobility group 20a. [refseq;acc:nm_018200] 1 208.588 171.778 1.21429
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 1.33501
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Squared 0 10.3503 19.2071 1.8557
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] Ranked 22038 18578 1.18624
pp3111 protein. [refseq;acc:nm_022156] Rooted 28.0891 23.0217 1.22011
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Measured 1095.42 812.166 1.34876
ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050] Squared 1 189976 124480 1.52616
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Rooted 54.8203 67.934 1.23921

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/