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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1030 to 1079 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
258 Ranked max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 227.999 204.366 1.11564
Squared huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 76438 58889.7 1.29799
Rooted thrombospondin 3 precursor. [swissprot;acc:p49746] 51.6132 45.8422 1.12589
259 Measured neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 6417.81 7852.52 1.22355
Ranked max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 227.999 204.37 1.11562
Squared goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] 76360.8 58841.7 1.29773
Rooted tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] 58.2964 65.5926 1.12516
260 Measured signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 4244.95 5193.42 1.22343
Ranked c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 219.421 196.978 1.11394
Squared huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] 76296.4 58801.6 1.29752
Rooted multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 59.0951 66.4332 1.12417
261 Measured signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 4247.36 5192.61 1.22255
Ranked heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 219.421 196.978 1.11394
Squared pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] 48127.9 62245.6 1.29334
Rooted ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 62.3337 70.0738 1.12417
262 Measured cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 24896.4 20431.7 1.21852
Ranked heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 219.421 196.978 1.11394
Squared neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] 26157.6 20236.2 1.29261
Rooted polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 59.4073 66.7002 1.12276
263 Measured trs85 homolog. [swissprot;acc:q9y2l5] 24896.4 20431.7 1.21852
Ranked heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 219.421 196.978 1.11394
Squared adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] 26157.6 20236.2 1.29261
Rooted paxillin. [swissprot;acc:p49023] 59.4073 66.7002 1.12276
264 Measured cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 4987.58 4094.57 1.2181
Ranked mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 219.421 196.978 1.11394
Squared adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] 26157.6 20236.2 1.29261
Rooted wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 66.1122 74.1438 1.12148
265 Measured wd-repeat protein wdc146. [swissprot;acc:q9c0j8] 24806.9 20369.9 1.21782
Ranked splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 225.217 202.459 1.11241
Squared leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 26157.6 20236.2 1.29261
Rooted u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 56.031 62.8281 1.12131
266 Measured cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] 24806.9 20369.9 1.21782
Ranked transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 241.07 267.88 1.11121
Squared fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] 26157.6 20236.2 1.29261
Rooted proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 66.1064 74.1074 1.12103
267 Measured ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 14021.4 11523 1.21682
Ranked density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 241.07 267.88 1.11121
Squared leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] 26157.6 20236.2 1.29261
Rooted tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 66.1064 74.1073 1.12103
268 Measured cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 24473.9 20127.8 1.21593
Ranked eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 271.016 244.167 1.10996
Squared laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 26157.6 20236.2 1.29261
Rooted proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 66.1064 74.1074 1.12103
269 Measured u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 4590.18 5575.52 1.21466
Ranked cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 241.373 267.352 1.10763
Squared thymic stromal co-transporter. [refseq;acc:nm_033051] 26157.6 20236.2 1.29261
Rooted tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] 66.1064 74.1074 1.12103
270 Measured fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 23640.2 19479.8 1.21358
Ranked fad synthetase. [refseq;acc:nm_025207] 241.373 267.352 1.10763
Squared transcription factor iib. [refseq;acc:nm_013242] 64739.9 50300.6 1.28706

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/