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 2125 to 2174 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
532 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Squared 28967 34626.4 1.19537
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Rooted 107.961 117.197 1.08555
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Measured 4651.88 5296.78 1.13863
zinc finger-like protein 9. [refseq;acc:nm_033414] Ranked 250.942 235.004 1.06782
533 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Rooted 50.8036 46.8198 1.08509
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Ranked 250.942 235.004 1.06782
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Measured 4651.88 5296.78 1.13863
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Squared 28937.1 34588.8 1.19531
534 40s ribosomal protein s16. [swissprot;acc:p17008] Rooted 50.8036 46.8198 1.08509
dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] Squared 27034.1 32301.8 1.19485
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Ranked 250.942 235.004 1.06782
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Measured 4651.88 5296.78 1.13863
535 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Rooted 50.8041 46.8218 1.08505
dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Ranked 236.662 252.708 1.0678
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Squared 37147.5 44372.1 1.19448
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Measured 10603.5 12069.5 1.13826
536 calsyntenin-1 precursor. [swissprot;acc:o94985]
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Rooted 66.0815 71.6562 1.08436
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Squared 28657.6 34208.6 1.1937
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Ranked 242.531 227.136 1.06778
537 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Rooted 66.0817 71.6545 1.08433
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Squared 28657.6 34208.6 1.1937
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Ranked 229.803 215.301 1.06736
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Measured 10603.5 12069.5 1.13826
538 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] Ranked 237.627 253.604 1.06724
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Rooted 66.0817 71.6543 1.08433
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Squared 28657.6 34208.6 1.1937
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Measured 10603.5 12069.4 1.13825
539 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Rooted 66.0818 71.6537 1.08432
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Ranked 236.964 252.86 1.06708
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Measured 10603.5 12069.4 1.13825
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Squared 20613.1 24595.9 1.19322
540 argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 26048.6 31057.4 1.19229
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Rooted 66.082 71.6526 1.0843
gk001 protein. [refseq;acc:nm_020198] Measured 10603.5 12069.4 1.13825
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Ranked 222.156 208.201 1.06703
541 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Measured 10600.3 12065.2 1.13819
coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Squared 53774.6 45105.5 1.1922
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Ranked 222.156 208.201 1.06703
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Rooted 66.082 71.6526 1.0843
542 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Ranked 222.156 208.201 1.06703
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Measured 3889.27 4426.74 1.13819
s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] Squared 26084.2 31084.3 1.19169
543 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Measured 10599.9 12064.7 1.13819
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Rooted 66.082 71.6525 1.0843
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Squared 26612.5 31709 1.19151
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Ranked 222.156 208.201 1.06703
544 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Rooted 66.082 71.6525 1.0843
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Ranked 222.156 208.201 1.06703

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/