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.


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 [...,...].
Gene Rank Value Type Network Comparison Type description green Filtered red Interaction Map network_comparison
Results: HTML CSV LaTeX Showing element 951 to 1000 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
green
Filtered
red
Interaction Map
network_comparison
238 rd protein. [swissprot;acc:p18615] 254.15 1 227.357 High confidence 1.11785
similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_145287] 4853.29 0 4256.39 Low confidence 1.14024
239 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] 201.086 1 210.504 1.04684
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 254.15 227.357 High confidence 1.11785
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 9795.36 0 8907.41 1.09969
similar to zinc finger protein 136. [refseq;acc:nm_145295] 4853.29 4256.39 Low confidence 1.14024
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 254.15 1 227.357 High confidence 1.11785
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 155.476 162.755 Low confidence 1.04682
methyltransferase like 2. [refseq;acc:nm_018396] 16326 0 17946 High confidence 1.09923
similar to dna-binding protein; zinc finger protein 253. [refseq;acc:nm_145297] 4853.29 4256.39 Low confidence 1.14024
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] 254.15 1 227.357 High confidence 1.11785
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 155.476 162.755 Low confidence 1.04682
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 12743.3 0 14003.7 High confidence 1.09891
zinc finger protein 132. [swissprot;acc:p52740] 4853.03 4256.15 Low confidence 1.14024
242 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 13895.8 15260.6 High confidence 1.09822
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 155.476 1 162.755 Low confidence 1.04682
j domain containing protein 1. [swissprot;acc:q9ukb3] 254.15 227.357 High confidence 1.11785
zinc finger protein 84 (zinc finger protein hpf2). [swissprot;acc:p51523] 4853.29 0 4256.39 Low confidence 1.14024
243 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 155.476 1 162.755 1.04682
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] 1373 0 1251 High confidence 1.09752
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 254.15 1 227.357 1.11785
zinc finger protein 121 (zinc finger protein 20) (fragment). [swissprot;acc:p58317] 4853.62 0 4256.71 Low confidence 1.14023
244 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 254.15 1 227.357 High confidence 1.11785
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 155.476 162.755 Low confidence 1.04682
keratin associated protein 9.2. [refseq;acc:nm_031961] 11579.9 0 10551.1 High confidence 1.09751
zinc finger protein af020591. [refseq;acc:nm_014480] 4853.87 4256.94 Low confidence 1.14023
245 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 13019 11867.6 High confidence 1.09702
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 155.476 1 162.755 Low confidence 1.04682
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 202.333 226.109 High confidence 1.11751
zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [swissprot;acc:p17024] 4853.87 0 4256.94 Low confidence 1.14023
246 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 212.363 1 237.312 High confidence 1.11748
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 155.476 162.755 Low confidence 1.04682
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 11573.7 0 10551.6 High confidence 1.09687
zinc finger protein 11b (fragment). [swissprot;acc:q06732] 4853.45 4256.55 Low confidence 1.14023
247 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 155.476 1 162.755 1.04682
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] 11573.7 0 10551.6 High confidence 1.09687
rna-binding protein. [refseq;acc:nm_019027] 212.41 1 237.302 1.11719
zinc finger protein 208. [swissprot;acc:o43345] 4853.87 0 4256.94 Low confidence 1.14023
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 212.41 1 237.302 High confidence 1.11719
keratin associated protein 1.5. [refseq;acc:nm_031957] 11573.7 0 10551.6 1.09687
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 155.476 1 162.755 Low confidence 1.04682
zinc finger protein 136. [swissprot;acc:p52737] 4853.62 0 4256.71 1.14023
249 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] 201.076 1 210.487 1.0468
gonadotropin inducible transcription repressor-1 (giot-1). [swissprot;acc:q8taf7] 4854.04 0 4257.1 1.14022
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 11573.7 10551.6 High confidence 1.09687
ns1-associated protein 1. [refseq;acc:nm_006372] 212.41 1 237.302 1.11719
250 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] 201.051 210.443 Low confidence 1.04671
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 212.41 237.302 High confidence 1.11719
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 11573.7 0 10551.6 1.09687
zinc finger protein 85 (zinc finger protein hpf4) (htf1). [swissprot;acc:q03923] 4854.21 4257.26 Low confidence 1.14022

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/