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 8191 to 8240 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : Low confidence
Filtered  : 1
Rank
description
red
green
network_comparison
4963 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] 201.297 201.493 1.00097
4964 dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] 201.299 201.494
4965 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 204.218 204.415 1.00096
4966 kelch-like protein x. [swissprot;acc:q9y2m5] 205.621 205.429 1.00093
4967 smooth muscle cell associated protein-1. [refseq;acc:nm_017979] 201.437 201.62 1.00091
4968 dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] 201.324 201.507
4969 shc transforming protein. [swissprot;acc:p29353] 205.086 205.268 1.00089
4970 myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, drosophila). [refseq;acc:nm_182931] 201.904 202.084
4971 kinesin-like protein kif3c. [swissprot;acc:o14782] 194.036 193.866 1.00088
4972 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 197.202 197.037 1.00084
4973 retinol dehydrogenase 13 (all-trans and 9-cis); retinol dehydrogenase 13. [refseq;acc:nm_138412] 203.232 203.064 1.00083
4974 ring finger protein 3. [refseq;acc:nm_006315] 201.294 201.133 1.0008
4975 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 202.363 202.202
4976 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 197.195 197.038
4977 dna excision repair protein ercc-1. [swissprot;acc:p07992] 203.61 203.773
4978 origin recognition complex subunit 2. [swissprot;acc:q13416] 196.037 196.184 1.00075
4979 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] 198.629 198.483 1.00074
4980 vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] 202.703 202.557 1.00072
4981 kinesin-like protein kif3a (microtubule plus end-directed kinesin motor 3a). [swissprot;acc:q9y496] 193.278 193.418
4982 neuronal shc. [refseq;acc:nm_016848] 205.038 205.174 1.00066
4983 protein sck (fragment). [swissprot;acc:p98077] 205.037 205.171 1.00065
4984 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] 202.785 202.913 1.00063
4985 fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] 198.253 198.368 1.00058
4986 fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] 198.568 198.464 1.00052
4987 myelin p2 protein. [swissprot;acc:p02689] 198.567
4988 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] 203.626 203.525 1.0005
4989 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] 202.023 202.108 1.00042
4990 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 203.148 203.233
4991 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] 205.526 205.451 1.00037
4992 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 206.266 206.342
4993 dual specificity protein kinase ttk (ec 2.7.1.-) (pyt). [swissprot;acc:p33981] 193.792 193.722 1.00036
4994 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 203.12 203.189 1.00034
4995 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 199.861 199.798 1.00032
4996 suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524] 210.227 210.162 1.00031
4997 cytohesin 4. [swissprot;acc:q9uia0] 177.9 177.845
4998 polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947] 199.669 199.609 1.0003
4999 g protein-coupled receptor kinase grk4 (ec 2.7.1.-) (iti1). [swissprot;acc:p32298] 203.07 203.131
5000 g protein-coupled receptor kinase grk5 (ec 2.7.1.-) (g-protein-coupled receptor kinase 5). [swissprot;acc:p34947]
5001 rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]
5002 g protein-coupled receptor kinase grk6 (ec 2.7.1.-) (g-protein-coupled receptor kinase 6). [swissprot;acc:p43250]
5003 fad synthetase. [refseq;acc:nm_025207] 204.534 204.591 1.00028
5004 thousand and one amino acid protein kinase. [refseq;acc:nm_004783] 208.596 208.556 1.00019
5005 ste20-like kinase; ste2-like kinase. [refseq;acc:nm_016281]
5006 tektin 2 (tektin-t) (testicular tektin b1-like protein). [swissprot;acc:q9uif3]
5007 trinucleotide repeat containing 6; edie; gw182 autoantigen. [refseq;acc:nm_014494]
5008 rb1-inducible coiled coil protein 1. [refseq;acc:nm_014781]
5009 macrophage mannose receptor precursor (mmr) (cd206 antigen). [swissprot;acc:p22897] 205.102 205.132 1.00015
5010 phospholipase a2 receptor 1, 180kda; phospholipase a2 receptor 1, 180kd. [refseq;acc:nm_007366]
5011 serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] 205.104 205.135
5012 ganglioside induced differentiation associated protein 2; likely ortholog of mouse ganglioside-induced differentiation-associated-protein 2. [refseq;acc:nm_017686] 192.907 192.879

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/