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 1275 to 1324 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
638 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] Low confidence 203.825 198.081 1.029
sorting nexin 17. [swissprot;acc:q15036] High confidence 228.639 242.258 1.05957
639 nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] 217.67 230.596 1.05938
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Low confidence 204.933 199.164 1.02897
640 intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] High confidence 217.67 230.596 1.05938
megf6 (fragment). [sptrembl;acc:o75095] Low confidence 207.235 201.402 1.02896
641 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] High confidence 217.67 230.596 1.05938
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence 198.493 192.907 1.02896
642 cullin homolog 2 (cul-2). [swissprot;acc:q13617] 203.883 198.148 1.02894
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] High confidence 217.67 230.596 1.05938
643 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Low confidence 203.104 197.399 1.0289
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] High confidence 217.67 230.596 1.05938
644 cgthba protein (-14 gene protein). [swissprot;acc:q12980]
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Low confidence 203.911 198.193 1.02885
645 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] High confidence 217.67 230.596 1.05938
protein disulfide isomerase a2 precursor (ec 5.3.4.1) (pdip). [swissprot;acc:q13087] Low confidence 204.488 198.765 1.02879
646 short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] High confidence 216.731 229.549 1.05914
transcription factor btf3 homolog 1. [swissprot;acc:q13890] Low confidence 204.634 198.914 1.02876
647 brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 203.293 197.621 1.0287
dynein light chain 2. [refseq;acc:nm_080677] High confidence 216.731 229.549 1.05914
648 aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353] Low confidence 210.325 216.359 1.02869
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] High confidence 218.227 206.078 1.05895
649 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Low confidence 203.283 197.617 1.02867
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] High confidence 233.725 220.751 1.05877
650 similar to s. cerevisiae ssm4. [refseq;acc:nm_005885] Low confidence 207.662 201.876 1.02866
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] High confidence 228.986 216.276 1.05877
651 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 233.725 220.751
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Low confidence 207.662 201.876 1.02866
652 tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] High confidence 248.994 235.255 1.0584
zinc finger protein t86. [swissprot;acc:o00488] Low confidence 205.897 200.163 1.02865
653 dihydroorotate dehydrogenase, mitochondrial precursor (ec 1.3.3.1) (dihydroorotate oxidase) (dhodehase) (fragment). [swissprot;acc:q02127] 203.975 198.304 1.0286
dok-like protein. [refseq;acc:nm_024872] High confidence 216.504 204.622 1.05807
654 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Low confidence 205.995 200.27 1.02859
655 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] High confidence 216.504 204.622 1.05807
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Low confidence 205.995 200.27 1.02859
656 integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [swissprot;acc:p05107] 206.339 200.608 1.02857
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] High confidence 216.504 204.622 1.05807
657 integrin beta-7 precursor. [swissprot;acc:p26010] Low confidence 206.341 200.609 1.02857
synapsin iii. [swissprot;acc:o14994] High confidence 229.072 216.576 1.0577
658 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] Low confidence 206.342 200.61 1.02857
659 hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] High confidence 229.072 216.576 1.0577
tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881] Low confidence 175.504 170.633 1.02855
660 actin binding lim protein 2. [refseq;acc:nm_032432] High confidence 229.072 216.576 1.0577
integrin alpha-7 precursor. [swissprot;acc:q13683] Low confidence 206.32 200.601 1.02851
661 hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] High confidence 229.072 216.576 1.0577
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Low confidence 200.62 195.059 1.02851
662 integrin alpha-6 precursor (vla-6) (cd49f). [swissprot;acc:p23229] 206.321 200.601
synapsin ii. [swissprot;acc:q92777] High confidence 229.072 216.576 1.0577

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/