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 1080 to 1129 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
540 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Subtracted 6228.39 7013.19 784.8
541 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Divided 10600.3 12065.2 1.13819
limkain b1. [refseq;acc:nm_019081] Subtracted 6228.39 7013.19 784.8
542 putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Divided 3889.27 4426.74 1.13819
543 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 10599.9 12064.7
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Subtracted 6228.39 7013.19 784.8
544 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Divided 3889.27 4426.74 1.13819
545 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Subtracted 6228.39 7013.19 784.8
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Divided 3889.27 4426.74 1.13819
546 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Subtracted 6228.39 7013.19 784.8
zinc finger protein t86. [swissprot;acc:o00488] Divided 4052.77 4612.54 1.13812
547 ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Subtracted 6228.39 7013.19 784.8
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Divided 5291.92 6020.19 1.13762
548 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 8268.19 9405.85 1.13759
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Subtracted 6228.39 7013.19 784.8
549 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Divided 5865.79 6671.23 1.13731
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Subtracted 6228.42 7013.21 784.79
550 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 6228.97 7013.53 784.56
prohibitin. [swissprot;acc:p35232] Divided 5773.45 6563.69 1.13687
551 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Subtracted 6503.1 7282.94 779.84
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Divided 5773.45 6563.69 1.13687
552 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Subtracted 6503.03 7282.5 779.47
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Divided 15427.2 13572.8 1.13663
553 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Subtracted 10430.3 9656.4 773.9
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Divided 3853.64 4379.71 1.13651
554 dendritic cell protein. [refseq;acc:nm_006360] Subtracted 6593.17 7364.55 771.38
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Divided 14830.5 13050.3 1.13641
555 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Subtracted 6593.17 7364.55 771.38
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Divided 6167.93 7007.7 1.13615
556 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Subtracted 6593.17 7364.55 771.38
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Divided 6167.93 7007.7 1.13615
557 cpz gene product. [refseq;acc:nm_003652] Subtracted 6593.17 7364.55 771.38
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Divided 6167.93 7007.7 1.13615
558 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Subtracted 6593.17 7364.55 771.38
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Divided 6167.93 7007.7 1.13615
559 inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Subtracted 6593.17 7364.55 771.38
560 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Divided 5480.24 6222.04 1.13536
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Subtracted 6374.65 7145.59 770.94
561 transforming protein rhoc (h9). [swissprot;acc:p08134] Divided 5480.24 6222.04 1.13536
tubby protein homolog. [swissprot;acc:p50607] Subtracted 6374.65 7145.59 770.94
562 protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Divided 5480.24 6222.04 1.13536
563 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Subtracted 6374.65 7145.59 770.94
564 tbc1 domain family member 5. [swissprot;acc:q92609]
transforming protein rhoa (h12). [swissprot;acc:p06749] Divided 5480.24 6222.04 1.13536
565 small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] 10434.4 11846.2 1.1353

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/