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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7412 to 7461 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1853 phosphatidylinositol 3,4,5-trisphosphate-dependent rac exchanger 1 protein (p-rex1 protein). [swissprot;acc:q8tcu6] Divided Low confidence 7987.2 8248.34 1.03269
1854 gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] Subtracted 8152.52 8412.93 260.41
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Divided High confidence 6076.66 6463.14 1.0636
mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Subtracted 5458.12 5830.76 372.64
similar to phosphatidylinositol 4-kinase, catalytic, alpha polypeptide. [sptrembl;acc:q8wuk7] Divided Low confidence 8222.95 8491.65 1.03268
1855 fasciculation and elongation protein zeta 2 (zygin ii). [swissprot;acc:q9uhy8] Subtracted 7978.55 8238.87 260.32
integrin alpha-7 precursor. [swissprot;acc:q13683] Divided 7833.62 8089.65 1.03268
keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] High confidence 6076.66 6463.14 1.0636
n-acetylglutamate synthase. [refseq;acc:nm_153006] Subtracted 5162.27 5534.71 372.44
1856 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Low confidence 7965.28 8225.58 260.3
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Divided High confidence 6076.66 6463.14 1.0636
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Low confidence 8114.52 8379.71 1.03268
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Subtracted High confidence 4413.55 4784.6 371.05
1857 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] Divided Low confidence 7965.28 8225.58 1.03268
golgi apparatus protein 1 precursor (golgi sialoglycoprotein mg-160) (e-selectin ligand 1) (esl-1) (cysteine-rich fibroblast growth factor receptor) (cfr-1). [swissprot;acc:q92896] Subtracted 260.3
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Divided High confidence 6076.66 6463.15 1.0636
transportin-sr; importin 12. [refseq;acc:nm_012470] Subtracted 5184.94 5555.76 370.82
1858 integrin alpha-6 precursor (vla-6) (cd49f). [swissprot;acc:p23229] Divided Low confidence 7833.58 8089.62 1.03268
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] High confidence 6076.66 6463.13 1.0636
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Subtracted Low confidence 8025.12 8285.35 260.23
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] High confidence 5882.1 6252.66 370.56
1859 golgi apparatus protein 1 precursor (golgi sialoglycoprotein mg-160) (e-selectin ligand 1) (esl-1) (cysteine-rich fibroblast growth factor receptor) (cfr-1). [swissprot;acc:q92896] Divided Low confidence 7965.28 8225.58 1.03268
heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] Subtracted High confidence 5733.71 6104.26 370.55
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Divided 6076.66 6463.13 1.0636
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Subtracted Low confidence 8025.12 8285.35 260.23
1860 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] High confidence 5184.45 5554.97 370.52
integrin alpha-3 precursor (galactoprotein b3) (gapb3) (vla-3 alpha chain) (cd49c). [swissprot;acc:p26006] Divided Low confidence 7833.64 8089.67 1.03268
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] High confidence 6076.66 6463.13 1.0636
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Subtracted Low confidence 7770.17 8030.31 260.14
1861 brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] 8017.54 8277.57 260.03
keratin associated protein 1.5. [refseq;acc:nm_031957] Divided High confidence 6076.66 6463.14 1.0636
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Subtracted 4331.35 4700.91 369.56
zinc finger protein t86. [swissprot;acc:o00488] Divided Low confidence 7864.01 8120.92 1.03267
1862 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] Subtracted High confidence 5826 6195.48 369.48
conserved oligomeric golgi complex component 1. [swissprot;acc:q8wtw3] Low confidence 8165.8 8425.81 260.01
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Divided 8162.16 8428.82 1.03267
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] High confidence 6076.66 6463.13 1.0636
1863 15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] Subtracted Low confidence 8165.8 8425.81 260.01
adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] High confidence 5826 6195.48 369.48
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Divided Low confidence 8081.38 8345.43 1.03267
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] High confidence 6076.66 6463.14 1.0636
1864 fasciculation and elongation protein zeta 1 (zygin i). [swissprot;acc:q99689] Low confidence 7979.57 8240.15 1.03266
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] High confidence 6076.66 6463.14 1.0636
peptide deformylase, mitochondrial precursor (ec 3.5.1.88) (pdf) (polypeptide deformylase). [swissprot;acc:q9hbh1] Subtracted Low confidence 8165.8 8425.81 260.01
ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] High confidence 5826 6195.48 369.48
1865 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] Divided Low confidence 7947.06 8206.59 1.03266
metastasis-associated protein mta1. [swissprot;acc:q13330] Subtracted 7697.8 7957.79 259.99
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] High confidence 5826 6195.48 369.48
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Divided 6076.66 6463.12 1.0636
1866 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Subtracted Low confidence 8018.4 8278.28 259.88

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/