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 4130 to 4179 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
517 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Rooted Subtracted 93.6382 88.4565 5.1817
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Measured Divided 4910.6 5600.61 1.14051
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Subtracted 1153.5 339.5 814
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Squared 31100.2 36086.5 4986.3
metaxin 2. [swissprot;acc:o75431] Ranked Divided 219.537 234.793 1.06949
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Subtracted 248.463 234.095 14.368
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Squared Divided 19263.3 23092.3 1.19877
518 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Rooted Subtracted 93.5947 88.4244 5.1703
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Squared 31100.1 36086.4 4986.3
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Ranked Divided 250.858 234.563 1.06947
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Squared 11447.3 13719.2 1.19847
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Ranked Subtracted 218.596 204.344 14.252
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Measured 1153.5 339.5 814
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Rooted Divided 50.0578 54.5502 1.08974
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Measured 4910.6 5600.61 1.14051
519 db83 protein. [swissprot;acc:p57088] Subtracted 1153.5 339.5 814
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Rooted 93.5901 88.4209 5.1692
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Measured Divided 9648.27 10994.9 1.13957
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Squared Subtracted 31100.1 36086.4 4986.3
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Divided 22387.1 26827.3 1.19834
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Ranked Subtracted 218.613 204.382 14.231
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Divided 218.702 204.582 1.06902
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Rooted 114.309 124.527 1.08939
520 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 61.1902 66.6503 1.08923
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Subtracted 93.5619 88.4001 5.1618
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Measured Divided 9642.22 10986.4 1.13941
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Subtracted 3858.52 4669.27 810.75
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Squared 31100.1 36086.4 4986.3
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Ranked 223.356 209.149 14.207
paxillin. [swissprot;acc:p49023] Squared Divided 22387.1 26827.3 1.19834
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Ranked 214.754 229.565 1.06897
521 carboxypeptidase a5. [refseq;acc:nm_080385] Squared 53174 44377.4 1.19822
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Rooted 61.1902 66.6503 1.08923
exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Ranked 215.237 230.07 1.06891
keratin associated protein 1.5. [refseq;acc:nm_031957] Squared Subtracted 31100.2 36086.5 4986.3
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Rooted 49.5225 54.6817 5.1592
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Measured 6143.52 6950.75 807.23
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Ranked 218.702 204.582 14.12
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Measured Divided 5390.78 6142.07 1.13937
522 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Subtracted 6148.94 6955.76 806.82
carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Squared Divided 53174 44377.4 1.19822
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Rooted Subtracted 51.7959 56.9253 5.1294
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Measured Divided 9634.98 10976.2 1.1392
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Ranked 222.893 208.523 1.06891
septin 10 isoform 1. [refseq;acc:nm_144710] Rooted 113.733 123.871 1.08914
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Ranked Subtracted 229.709 215.631 14.078
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Squared 31100.1 36086.4 4986.3
523 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Measured Divided 10640.2 12117.8 1.13887
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Subtracted 5865.79 6671.23 805.44
exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Ranked Divided 215.237 230.07 1.06891

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/