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 4158 to 4207 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
520 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Ranked Subtracted 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
histone h2b.c (h2b/c). [swissprot;acc:q99880] Subtracted 247.47 233.441 14.029
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Squared 31100.2 36086.5 4986.3
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Divided 53174 44377.4 1.19822
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Rooted 66.377 72.2842 1.08899
zinc finger-like protein 9. [refseq;acc:nm_033414] Subtracted 49.3451 54.4606 5.1155
524 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Squared Divided 53174 44377.4 1.19822
aquaporin 5. [swissprot;acc:p55064] Measured 10640 12117.6 1.13887
brain protein 44. [swissprot;acc:o95563] Rooted 113.374 123.463 1.08899
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Ranked 215.237 230.07 1.06891
histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778] Subtracted 247.47 233.441 14.029
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Squared 31100.2 36086.5 4986.3
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Rooted 49.3451 54.4606 5.1155
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] Measured 5206.9 6010.04 803.14
525 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Squared Divided 53174 44377.4 1.19822
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Ranked 215.237 230.07 1.06891
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Rooted Subtracted 49.3451 54.4606 5.1155
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Ranked 247.47 233.441 14.029
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Measured Divided 10639.8 12117.3 1.13887
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5] Subtracted 5207.03 6010.1 803.07
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Rooted Divided 113.374 123.463 1.08899
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Squared Subtracted 31100.1 36086.4 4986.3
526 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Measured Divided 10639.9 12117.4 1.13886
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Rooted Subtracted 49.0882 54.2027 5.1145
electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Squared Divided 31189.6 37352.8 1.1976
histone h2b. [refseq;acc:nm_175055] Ranked Subtracted 247.47 233.441 14.029
keratin associated protein 4.4. [refseq;acc:nm_032524] Squared 31100.2 36086.5 4986.3
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Ranked Divided 250.538 234.401 1.06884
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Measured Subtracted 5207.78 6010.45 802.67

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/