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 851 to 900 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
426 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 1 5942.49 6853.15 1.15325
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 0 2071.59 2133.83 1.03004
427 putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 1195.87 1161.29 1.02978
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 1 11736.6 13531.9 1.15297
428 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] 0 14267.5 14688.8 1.02953
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 1 3721.19 4288.17 1.15237
429 tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] 0 472.351 485.852 1.02858
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] 1 6272.91 7226.06 1.15195
430 succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 0 10247.8 10535 1.02803
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 1 3804.09 4379.37 1.15123
431 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 3849.94 4431.36 1.15102
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 0 146.622 150.709 1.02787
432 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9] 100.5 103.25 1.02736
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] 1 5244.71 6036.27 1.15093
433 mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] 5244.88 6036.38 1.15091
sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3] 0 100.5 103.25 1.02736
434 testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] 201 206.5
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] 1 5246.38 6037.37 1.15077
435 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] 0 5891.28 5737.71 1.02677
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 1 5233.86 6022.6 1.1507
436 alpha-nac protein. [sptrembl;acc:q9h009] 0 147.221 151.122 1.0265
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 1 6230.94 7168.2 1.15042
437 protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] 0 2331 2390 1.02531
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 1 3779.92 4348.48 1.15042
438 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 0 2925.57 2853.65 1.0252
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] 1 6252.58 7192.88 1.15039
439 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] 0 532.667 546 1.02503
440 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 1 6251.91 7192.08 1.15038
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] 0 6830.67 7000.85 1.02491
441 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 6158 6303 1.02355
grancalcin. [swissprot;acc:p28676] 1 6251.96 7192.13 1.15038
442 repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] 0 6699.82 6856.28 1.02335
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 1 6251.99 7192.17 1.15038
443 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 6252.27 7192.51
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 0 2432.41 2379.52 1.02223
444 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 2431.87 2378.99
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 1 3758.67 4322.87 1.15011
445 ad24 protein. [refseq;acc:nm_022451] 3753.71 4315.95 1.14978
mstp028 protein. [refseq;acc:nm_031954] 0 9988.45 9808.48 1.01835
446 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 1549.26 1522.06 1.01787
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 1 3766.03 4329.37 1.14958
447 40s ribosomal protein s3a. [swissprot;acc:p49241] 0 2929.51 2879.55 1.01735
pescadillo homolog 1. [swissprot;acc:o00541] 1 3751.14 4310.89 1.14922
448 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 6259.3 7190.91 1.14884
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 0 524.415 533.236 1.01682
449 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 5699.32 5607.7 1.01634
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 1 3761.59 4319.69 1.14837
450 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 0 4158.33 4094.09 1.01569
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] 1 4889.21 5610.52 1.14753

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/