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 Hugo Value Type description 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
Hugo
Value Type
description
red
green
network_comparison
532 PRODH2 Squared kidney and liver proline oxidase 1. [refseq;acc:nm_021232] 28967 34626.4 1.19537
SEPT4 Rooted 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] 107.961 117.197 1.08555
ZNF622 Ranked zinc finger-like protein 9. [refseq;acc:nm_033414] 250.942 235.004 1.06782
ZNHIT3 Measured thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] 4651.88 5296.78 1.13863
533 MRPL13 Rooted 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] 50.8036 46.8198 1.08509
NHP2L1 Measured 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] 4651.88 5296.78 1.13863
SLC45A2 Ranked membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] 250.942 235.004 1.06782
SLC5A5 Squared sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] 28937.1 34588.8 1.19531
534 no value Ranked guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] 250.942 235.004 1.06782
DHDDS Squared dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 27034.1 32301.8 1.19485
NUFIP1 Measured 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] 4651.88 5296.78 1.13863
RPS16 Rooted 40s ribosomal protein s16. [swissprot;acc:p17008] 50.8036 46.8198 1.08509
535 MPP3 Squared maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] 37147.5 44372.1 1.19448
POLR2H Ranked dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] 236.662 252.708 1.0678
RPL13A Rooted 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 50.8041 46.8218 1.08505
SSR4 Measured translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] 10603.5 12069.5 1.13826
536 CLSTN1 calsyntenin-1 precursor. [swissprot;acc:o94985]
HOXA10 Rooted homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 66.0815 71.6562 1.08436
ITM2B Squared integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] 28657.6 34208.6 1.1937
SSB Ranked lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] 242.531 227.136 1.06778
537 no value Measured 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] 10603.5 12069.5 1.13826
DHX15 Ranked putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 229.803 215.301 1.06736
HOXB9 Rooted homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 66.0817 71.6545 1.08433
ITM2C Squared integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] 28657.6 34208.6 1.1937
538 HOXA9 Rooted homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 66.0817 71.6543 1.08433
ITM2A Squared integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] 28657.6 34208.6 1.1937
POLR2L Ranked dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] 237.627 253.604 1.06724
PTPRB Measured protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] 10603.5 12069.4 1.13825
539 HOXC9 Rooted homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 66.0818 71.6537 1.08432
MEMO1P Ranked protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] 236.964 252.86 1.06708
PRSS16 Measured thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] 10603.5 12069.4 1.13825
WRNIP1 Squared werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] 20613.1 24595.9 1.19322
540 ASL argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] 26048.6 31057.4 1.19229
CCDC47 Measured gk001 protein. [refseq;acc:nm_020198] 10603.5 12069.4 1.13825
GABRG3 Rooted gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 66.082 71.6526 1.0843
SEPHS2 Ranked selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] 222.156 208.201 1.06703
541 CLSTN2 Measured calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 10600.3 12065.2 1.13819
COPB1 Squared coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] 53774.6 45105.5 1.1922
FOXG1 Rooted forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 66.082 71.6526 1.0843
MICAL2 Ranked flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] 222.156 208.201 1.06703
542 AKT1 Measured rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] 3889.27 4426.74 1.13819
GABRG1 Rooted gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 66.082 71.6526 1.0843
INPP4B Ranked inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] 222.156 208.201 1.06703
MAT1A Squared s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266] 26084.2 31084.3 1.19169
543 CLSTN3 Measured calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 10599.9 12064.7 1.13819
CNDP1 Squared glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] 26612.5 31709 1.19151
GABRA2 Rooted gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 66.082 71.6525 1.0843
SEPHS1 Ranked selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] 222.156 208.201 1.06703
544 AKT3 Measured rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] 3889.27 4426.74 1.13819
GABRA6 Rooted gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 66.082 71.6525 1.0843

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
- Hugo is the HGNC identifier if it exists
- 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/