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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1532 to 1581 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
766 protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] High confidence 213.804 224.226 1.04875
767 rho interacting protein 3. [refseq;acc:nm_015134] 213.803 224.224 1.04874
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Low confidence 206.437 201.034 1.02688
768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] High confidence 210.946 221.225 1.04873
ubiquitin-conjugating enzyme e2-32 kda complementing (ec 6.3.2.19) (ubiquitin-protein ligase) (ubiquitin carrier protein) (e2-cdc34). [swissprot;acc:p49427] Low confidence 199.792 194.573 1.02682
769 cab2. [refseq;acc:nm_033419] High confidence 210.946 221.225 1.04873
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Low confidence 198.33 193.155 1.02679
770 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] High confidence 210.946 221.225 1.04873
orphan nuclear receptor tr4 (orphan nuclear receptor tak1). [swissprot;acc:p49116] Low confidence 206.636 212.168 1.02677
771 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] High confidence 210.946 221.225 1.04873
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Low confidence 206.636 212.168 1.02677
772 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] High confidence 210.946 221.225 1.04873
protein phosphatase 1, regulatory (inhibitor) subunit 3b. [refseq;acc:nm_024607] Low confidence 203.48 198.181 1.02674
773 protein containing cxxc domain 2. [refseq;acc:nm_032590] 202.951 208.378
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] High confidence 210.946 221.225 1.04873
774 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 215.535 1.04854
ubiquitin associated protein 2 isoform 1; ad-012 protein. [refseq;acc:nm_018449] Low confidence 205.905 200.545 1.02673
775 histone deacetylase 2 (hd2). [swissprot;acc:q92769] High confidence 226.003 215.541 1.04854
transcription factor iib. [refseq;acc:nm_013242] Low confidence 205.668 200.313 1.02673
776 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] High confidence 225.996 215.535 1.04854
mad1-like 1; mad1 (mitotic arrest deficient, yeast, homolog)-like 1; mitotic-arrest deficient 1, yeast, homolog-like 1; tumor protein p53 inducible protein 9. [refseq;acc:nm_003550] Low confidence 208.017 202.601 1.02673
777 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] 204.807 199.484 1.02668
histone deacetylase 1 (hd1). [swissprot;acc:q13547] High confidence 225.989 215.53 1.04853
778 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] 209.191 219.332 1.04848
wd repeat domain 26. [refseq;acc:nm_025160] Low confidence 188.145 183.258 1.02667
779 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] 202.48 197.229 1.02662
deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] High confidence 230.516 241.641 1.04826
780 dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] 232.762 243.933 1.04799
importin 9. [refseq;acc:nm_018085] Low confidence 204.192 198.902 1.0266
781 protein arginine n-methyltransferase (ec 2.1.1.-). [swissprot;acc:q9nvm4] 203.591 198.319 1.02658
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] High confidence 245.84 257.636 1.04798
782 pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Low confidence 203.591 198.319 1.02658
translin. [swissprot;acc:q15631] High confidence 224.385 235.131 1.04789
783 porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Low confidence 204.238 198.951 1.02657
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] High confidence 224.385 235.131 1.04789
784 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Low confidence 201.338 196.126 1.02657
785 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] High confidence 244.447 233.508 1.04685
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Low confidence 202.469 197.233 1.02655
786 f-box and leucine-rich repeat protein 11; f-box protein fbl11. [refseq;acc:nm_012308] 202.957 208.337 1.02651
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] High confidence 244.447 233.508 1.04685
787 atpase, h+ transporting, lysosomal 42kda, v1 subunit c isoform 2; v-atpase c2 subunit. [refseq;acc:nm_144583] Low confidence 202.489 197.259 1.02651
down-regulated in metastasis. [refseq;acc:nm_014503] High confidence 244.447 233.508 1.04685
788 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Low confidence 200.788 195.605 1.0265
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] High confidence 138.705 132.538 1.04653
789 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 224.244 234.511 1.04578
polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481] Low confidence 205.859 200.547 1.02649
790 40s ribosomal protein s21. [swissprot;acc:p35265] High confidence 224.244 234.511 1.04578
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Low confidence 200.79 195.608 1.02649
791 cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] High confidence 224.244 234.511 1.04578

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/