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 1963 to 2012 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
491 rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] Divided 0 21970 21880 1.00411
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Subtracted 13692.7 13718.2 25.5
492 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 1 150.982 166.372 15.39
fibrillin 3. [refseq;acc:nm_032447] 0 930 953 23
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Divided 1 220.171 235.979 1.0718
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 0 6802.96 6829.74 1.00394
493 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Subtracted 11725.2 11748.1 22.9
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Divided 1 220.172 235.98 1.0718
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] 0 11999.1 12041.7 1.00355
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Subtracted 1 236.751 252.038 15.287
494 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 0 1543 1521 22
metaxin 2. [swissprot;acc:o75431] 1 219.537 234.793 15.256
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Divided 220.172 235.98 1.0718
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] 0 11985.5 11959.4 1.00218
495 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 11725.2 11748.1 1.00195
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 1 220.171 235.979 1.0718
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 0 772 754 18
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] 1 222.146 237.393 15.247
496 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 250.419 15.239
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Divided 250.938 234.134 1.07177
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] 0 9394 9411.49 1.00186
Subtracted 17.49
497 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 10231.8 10248.3 16.5
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Divided 1 251.344 234.514 1.07177
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 0 13692.7 13718.2 1.00186
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Subtracted 1 225.026 209.798 15.228
498 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Divided 0 10231.8 10248.3 1.00161
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Subtracted 9080.73 9069.58 11.15
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Divided 1 220.161 235.95 1.07172
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Subtracted 237.28 252.492 15.212
499 cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] 0 816 825 9
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] 1 237.28 252.492 15.212
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Divided 0 9080.73 9069.58 1.00123
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] 1 231.496 248.048 1.0715
500 huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] 0 394 394 1
Subtracted 0
inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Divided 1 224.662 240.673 1.07127
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Subtracted 237.28 252.492 15.212
501 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Divided 238.704 255.68 1.07112
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] 0 0.00001 0.00001 1
Subtracted 0 0 0
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] 1 237.28 252.492 15.212
502 brca1 associated protein. [refseq;acc:nm_006768] Divided 0 0.00001 0.00001 1
Subtracted 0 0 0
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Divided 1 238.704 255.68 1.07112
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Subtracted 237.28 252.492 15.212
503 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Divided 238.704 255.68 1.07112
504 homeobox protein barh-like 2. [swissprot;acc:q9umq3] Subtracted 237.28 252.492 15.212
oligophrenin 1. [swissprot;acc:o60890] Divided 238.704 255.68 1.07112

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/