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 Network Comparison Type description Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2513 to 2562 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
red
green
network_comparison
1257 Divided immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] 5438.66 5893.87 1.0837
Subtracted 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] 4254.62 4736.03 481.41
1258 Divided glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] 6251.32 6774.12 1.08363
Subtracted serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] 5961.97 6443.07 481.1
1259 Divided epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] 5685.38 6157.7 1.08308
Subtracted serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] 5961.97 6443.07 481.1
1260 Divided rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] 5754.84 6232.83 1.08306
Subtracted glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] 5961.97 6443.07 481.1
1261 Divided epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] 5685.34 6157.53 1.08305
Subtracted 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 6160.06 6640.78 480.72
1262 Divided serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] 5894.47 6383.73 1.083
Subtracted prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 5207.39 5687.2 479.81
1263 Divided gtp binding protein 2. [refseq;acc:nm_019096] 5894.47 6383.73 1.083
Subtracted prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] 5207.39 5687.2 479.81
1264 Divided cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] 5894.47 6383.73 1.083
Subtracted uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] 5207.39 5687.2 479.81
1265 Divided dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] 5894.47 6383.73 1.083
Subtracted 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 4250.54 4729.67 479.13
1266 Divided sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] 5894.47 6383.73 1.083
Subtracted mitotic checkpoint protein bub3. [swissprot;acc:o43684] 5470.44 5949.49 479.05
1267 Divided cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] 5894.47 6383.73 1.083
Subtracted zinc finger protein 207. [swissprot;acc:o43670] 5470.44 5949.49 479.05
1268 Divided sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] 5894.47 6383.73 1.083
Subtracted 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 4250.18 4729.12 478.94
1269 Divided xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] 5894.47 6383.73 1.083
Subtracted peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 7048.79 7527.42 478.63
1270 Divided epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] 5685.08 6156.48 1.08292
Subtracted daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 5654.53 6132.76 478.23
1271 Divided mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566] 5528.65 5985.58 1.08265
Subtracted retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] 5654.54 6132.69 478.15
1272 Divided pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 5528.65 5985.58 1.08265
Subtracted rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] 5754.84 6232.83 477.99
1273 Divided phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] 5885 6371.14 1.08261
Subtracted proteasome subunit alpha type 7 (ec 3.4.25.1) (proteasome subunit rc6-1) (proteasome subunit xapc7). [swissprot;acc:o14818] 6216.12 6693.38 477.26
1274 Divided 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] 5885 6371.14 1.08261
Subtracted megf6 (fragment). [sptrembl;acc:o75095] 5980.41 6457.51 477.1
1275 Divided 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] 5885 6371.14 1.08261
Subtracted proteasome subunit alpha type 7-like (ec 3.4.25.1). [swissprot;acc:q8taa3] 6216.13 6693.13 477
1276 Divided peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] 6437.99 6969.67 1.08258
Subtracted 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] 5988.06 6464.94 476.88
1277 Divided heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] 6437.99 6969.67 1.08258
Subtracted serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] 5418.33 5895.2 476.87
1278 Divided heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 6437.99 6969.67 1.08258
Subtracted eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 4131.04 4607.9 476.86
1279 Divided heat shock cognate 71 kda protein. [swissprot;acc:p11142] 6437.99 6969.67 1.08258
Subtracted eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] 4131.04 4607.9 476.86
1280 Divided dehydrodolichyl diphosphate synthase. [refseq;acc:nm_024887] 6350.81 6874.88 1.08252
Subtracted actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] 6036.22 6512.64 476.42
1281 Divided orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] 6230.49 6744.5 1.0825
Subtracted dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [swissprot;acc:q13561] 5322.16 5798.38 476.22

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/