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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Gene Rank Filtered description Network Comparison Type Value Type Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 3730 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Rank
Filtered
description
red
green
network_comparison
226 0 rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] 15395.7 16992.9 1.10374
1 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 239.991 269.238 1.12187
227 0 tigger transposable element derived 6. [refseq;acc:nm_030953] 12360 11200.2 1.10355
1 thrombospondin 3 precursor. [swissprot;acc:p49746] 239.99 269.234 1.12186
228 0 soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 10303.5 11370.4 1.10355
1 sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 226.411 202.088 1.12036
229 0 poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] 10899.4 9878.1 1.10339
1 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 226.401 202.094 1.12028
230 0 tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] 12364.7 11207.7 1.10323
1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 239.35 267.915 1.11934
231 0 tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 12364.8 11207.9 1.10322
1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 239.336 267.881 1.11927
232 0 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 12394.7 11240.2 1.10271
1 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 239.336 267.879 1.11926
233 0 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 9586.97 10560 1.1015
1 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 239.32 267.842 1.11918
234 0 transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 16614 18296 1.10124
1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] 287.41 256.835 1.11905
235 0 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 14554.5 16027.9 1.10123
1 phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 227.357 254.15 1.11785
236 0 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 15245.4 16788.5 1.10122
1 pp3111 protein. [refseq;acc:nm_022156] 227.357 254.15 1.11785
237 0 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 9984 9067 1.10114
1 syntaxin 18. [swissprot;acc:q9p2w9] 227.357 254.15 1.11785
238 0 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 12677.7 13941.7 1.0997
1 rd protein. [swissprot;acc:p18615] 227.357 254.15 1.11785
239 0 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 8907.41 9795.36 1.09969
1 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 227.357 254.15 1.11785
240 0 methyltransferase like 2. [refseq;acc:nm_018396] 17946 16326 1.09923
1 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 227.357 254.15 1.11785
241 0 secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 14003.7 12743.3 1.09891
1 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 227.357 254.15 1.11785
242 0 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 15260.6 13895.8 1.09822
1 j domain containing protein 1. [swissprot;acc:q9ukb3] 227.357 254.15 1.11785
243 0 polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1251 1373 1.09752
1 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 227.357 254.15 1.11785
244 0 keratin associated protein 9.2. [refseq;acc:nm_031961] 10551.1 11579.9 1.09751
1 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 227.357 254.15 1.11785
245 0 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 11867.6 13019 1.09702
1 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 226.109 202.333 1.11751
246 0 keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 10551.6 11573.7 1.09687
1 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 1.11748
247 0 keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] 10551.6 11573.7 1.09687
1 rna-binding protein. [refseq;acc:nm_019027] 237.302 212.41 1.11719
248 0 keratin associated protein 1.5. [refseq;acc:nm_031957] 10551.6 11573.7 1.09687
1 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 212.41 1.11719
249 0 keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 10551.6 11573.7 1.09687
1 ns1-associated protein 1. [refseq;acc:nm_006372] 237.302 212.41 1.11719
250 0 keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 10551.6 11573.7 1.09687
1 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 237.302 212.41 1.11719

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/