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 5658 to 5707 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1415 sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Squared 26893.1 30139.8 1.12073
stromal interaction molecule 2 precursor. [swissprot;acc:q9p246] Ranked 206.102 210.42 1.02095
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Rooted 52.359 50.3808 1.03926
1416 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Squared 26893.1 30139.8 1.12073
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Rooted 61.2971 63.7036 1.03926
serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286] Ranked 206.102 210.42 1.02095
xpmc2 prevents mitotic catastrophe 2 homolog; xenopus prevents mitotic catastrophe 2 homolog. [refseq;acc:nm_020385] Measured 6123.75 6597.71 1.0774
1417 carboxypeptidase a5. [refseq;acc:nm_080385] Ranked 203.979 208.229 1.02084
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Squared 26893.1 30139.8 1.12073
isocitrate dehydrogenase [nad] subunit alpha, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p50213] Measured 5360.39 5775.24 1.07739
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Rooted 65 67.552 1.03926
1418 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Ranked 203.979 208.229 1.02084
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] Rooted 52.359 50.3808 1.03926
isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837] Measured 5360.39 5775.24 1.07739
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Squared 26893.1 30139.8 1.12073
1419 isocitrate dehydrogenase [nad] subunit gamma, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:p51553] Measured 5360.39 5775.24 1.07739
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Ranked 203.979 208.229 1.02084
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Rooted 52.359 50.3808 1.03926
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Squared 26893.1 30139.8 1.12073
1420 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Ranked 203.979 208.229 1.02084
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Squared 16038 17973.3 1.12067
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Rooted 52.359 50.3808 1.03926
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Measured 5658.51 6096.21 1.07735
1421 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] Ranked 207.076 211.391 1.02084
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] Measured 5628.53 6063.61 1.0773
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622] Squared 27545 30868 1.12064
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Rooted 65 67.552 1.03926
1422 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Ranked 203.979 208.229 1.02084
gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936] Squared 27545 30868 1.12064
importin 8; ran-binding protein 8. [refseq;acc:nm_006390] Measured 5628.53 6063.61 1.0773
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Rooted 52.359 50.3808 1.03926
1423 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Measured 5628.53 6063.61 1.0773
cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Ranked 221.152 216.659 1.02074
d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] Rooted 65 67.552 1.03926
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196] Squared 27545 30868 1.12064
1424 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] Rooted 52.359 50.3808 1.03926
hsgcn1 (fragment). [sptrembl;acc:q99736] Measured 5628.53 6063.61 1.0773
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Ranked 214.717 219.157 1.02068
syntaxin 12. [refseq;acc:nm_177424] Squared 23940.9 26824.2 1.12043
1425 brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] Measured 5628.53 6063.61 1.0773
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Ranked 214.717 219.157 1.02068
homeobox protein barh-like 2. [swissprot;acc:q9umq3] Rooted 52.359 50.3808 1.03926
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Squared 22046.6 24692.8 1.12003
1426 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Ranked 214.717 219.157 1.02068
dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Squared 18713.9 20960.1 1.12003
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Rooted 61.2938 63.6979 1.03922
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Measured 5362.85 5777.33 1.07729
1427 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] Rooted 61.2934 63.6971 1.03922
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Squared 18756.5 21007.1 1.11999
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Ranked 214.717 219.157 1.02068

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/