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 4308 to 4357 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2154 vesicule-associated membrane protein 4 (vamp-4). [swissprot;acc:o75379] Divided 200.063 198.71 1.00681
2155 cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Subtracted 218.062 216.624 1.438
2156 adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Divided 200.063 198.71 1.00681
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] Subtracted 207.74 206.305 1.435
2157 nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [swissprot;acc:q92570] 207.743 206.308
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Divided 200.063 198.71 1.00681
2158 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] 206.401 207.796 1.00676
insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663] Subtracted 197.489 196.061 1.428
2159 mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] Divided 215.921 214.474 1.00675
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 122.3 123.727 1.427
2160 ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] Divided 215.925 214.481 1.00673
ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] Subtracted 219.377 220.8 1.423
2161 calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] Divided 215.925 214.481 1.00673
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [swissprot;acc:p43354] Subtracted 207.765 206.343 1.422
2162 calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] Divided 215.925 214.481 1.00673
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Subtracted 206.443 207.864 1.421
2163 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0]
mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] Divided 215.925 214.481 1.00673
2164 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Subtracted 206.443 207.864 1.421
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Divided 215.925 214.481 1.00673
2165 ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418]
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Subtracted 206.442 207.862 1.42
2166 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288] Divided 215.925 214.481 1.00673
band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Subtracted 206.442 207.862 1.42
2167 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]
glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] Divided 215.925 214.481 1.00673
2168 hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] Subtracted 221.842 223.246 1.404
mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [swissprot;acc:p28482] Divided 215.929 214.486 1.00673
2169 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] Subtracted 210.209 208.808 1.401
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357] Divided 215.925 214.481 1.00673
2170 fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Subtracted 221.509 220.108 1.401
ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [swissprot;acc:q9uk32] Divided 215.925 214.481 1.00673
2171 fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Subtracted 221.509 220.108 1.401
ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [swissprot;acc:q15349] Divided 215.925 214.481 1.00673
2172 calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7]
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Subtracted 221.509 220.108 1.401
2173 calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [swissprot;acc:q13554] Divided 215.925 214.481 1.00673
wd-repeat protein 4. [swissprot;acc:p57081] Subtracted 221.509 220.108 1.401
2174 mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] Divided 215.925 214.481 1.00673
myelin p2 protein. [swissprot;acc:p02689] Subtracted 221.509 220.108 1.401
2175 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] Divided 210.209 208.808 1.00671
kelch-like protein 8. [swissprot;acc:q9p2g9] Subtracted 221.509 220.108 1.401
2176 phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [swissprot;acc:p53350] Divided 218.089 216.64 1.00669
2177 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Subtracted 221.509 220.108 1.401
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Divided 210.961 209.563 1.00667
2178 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Subtracted 221.509 220.108 1.401
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Divided 210.961 209.563 1.00667
2179 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Subtracted 221.509 220.108 1.401

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/