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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 8964 to 9013 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2241 similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Squared 27045.6 29273.5 1.08238
2242 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Measured 3670.45 3504.91 1.04723
ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665] Squared 27045.6 29273.5 1.08238
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Ranked 209.197 207.915 1.00617
mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Rooted 69.5079 70.9754 1.02111
2243 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Squared 58316.6 53884.7 1.08225
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Measured 5776.96 6049.61 1.0472
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Ranked 209.197 207.915 1.00617
lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] Rooted 69.5079 70.9754 1.02111
2244 creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Squared 58381 53950.3 1.08213
gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] Measured 5776.96 6049.61 1.0472
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Ranked 209.197 207.915 1.00617
signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Rooted 86.4814 84.6942 1.0211
2245 acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 71.5599 73.0695
creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] Squared 58303.5 53878.8 1.08212
fibulin-2 precursor. [swissprot;acc:p98095] Ranked 191.618 190.448 1.00614
inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Measured 5776.96 6049.61 1.0472
2246 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 6209.77 6501.99 1.04706
mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] Ranked 223.58 224.943 1.0061
serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] Squared 27583.6 29846.1 1.08202
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Rooted 71.5497 73.0573 1.02107
2247 gtp binding protein 2. [refseq;acc:nm_019096] Squared 27583.6 29846.1 1.08202
rna-binding protein with multiple splicing (rbp-ms). [swissprot;acc:q93062] Measured 5819.36 6092.93 1.04701
sipl protein. [refseq;acc:nm_018269] Ranked 208.609 207.346 1.00609
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] Rooted 71.5497 73.0573 1.02107
2248 acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 71.5407 73.0465 1.02105
cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] Squared 27583.6 29846.1 1.08202
kinesin-like protein kif3c. [swissprot;acc:o14782] Ranked 219.045 220.377 1.00608
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] Measured 5833.01 6106.48 1.04688
2249 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 6834.03 7153.66 1.04677
dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] Squared 27583.6 29846.1 1.08202
lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] Rooted 71.0627 72.5534 1.02098
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Ranked 181.091 179.999 1.00607
2250 esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Measured 6834.03 7153.66 1.04677
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Ranked 164.064 165.058 1.00606
lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] Rooted 71.0656 72.5557 1.02097
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] Squared 27583.6 29846.1 1.08202
2251 cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850]
e-1 enzyme. [refseq;acc:nm_021204] Ranked 208.315 207.061 1.00606
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Rooted 71.0656 72.5557 1.02097
serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] Measured 6196.65 6486.12 1.04671
2252 arf gtpase-activating protein git2 (g protein-coupled receptor kinase- interactor 2). [swissprot;acc:q14161] 5840.54 6113.01 1.04665
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Ranked 217.185 218.498 1.00605
lim/homeobox protein lhx4. [swissprot;acc:q969g2] Rooted 71.069 72.5584 1.02096
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Squared 27583.6 29846.1 1.08202
2253 chromodomain y-like protein 2. [refseq;acc:nm_152342] Rooted 71.6145 73.1123 1.02091
kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] Ranked 219.047 220.371 1.00604
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Measured 3629.21 3467.48 1.04664
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Squared 27583.6 29846.1 1.08202
2254 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 22719.3 24581.5 1.08197

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/