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 7091 to 7140 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1773 spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] Ranked 223.032 225.739 1.01214
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] Rooted 71.372 73.6197 1.03149
1774 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Measured 5386.37 5744.89 1.06656
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Ranked 223.032 225.739 1.01214
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Squared 26625.9 29291.6 1.10012
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Rooted 71.372 73.6197 1.03149
1775 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] Squared 26621.3 29286.1 1.1001
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] Rooted 71.372 73.6197 1.03149
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Ranked 207.757 210.274 1.01212
zinc finger protein 258. [refseq;acc:nm_145310] Measured 5386.37 5744.89 1.06656
1776 neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Rooted 71.372 73.6197 1.03149
nucleoporin like 1. [refseq;acc:nm_014089] Ranked 216.878 214.286 1.0121
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Squared 30414.7 33457.2 1.10003
zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202] Measured 5386.37 5744.89 1.06656
1777 nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Squared 26908.6 29598.5 1.09996
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Ranked 216.878 214.286 1.0121
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Rooted 71.372 73.6197 1.03149
zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095] Measured 5386.37 5744.89 1.06656
1778 actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] Ranked 216.878 214.286 1.0121
elks protein. [refseq;acc:nm_015064] Squared 26908.6 29598.5 1.09996
nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494] Rooted 71.372 73.6197 1.03149
1779 branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] 63.9787 65.9936
conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2] Measured 5386.37 5744.89 1.06656
dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] Squared 11731 12903.2 1.09992
pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] Ranked 206.332 203.874 1.01206
1780 germ cell-less. [refseq;acc:nm_022471] 206.335 203.877
nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] Rooted 71.372 73.6197 1.03149
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Squared 29473.4 32415 1.09981
similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2] Measured 5386.37 5744.89 1.06656
1781 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Rooted 67.1463 69.2594 1.03147
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] Ranked 206.332 203.874 1.01206
proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786] Squared 28410 31244.9 1.09979
1782 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] 13245.8 14566.6 1.09971
hyporthetical protein mgc27169. [refseq;acc:nm_176782] Ranked 206.332 203.874 1.01206
rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Rooted 62.1036 64.058 1.03147
zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7] Measured 5386.37 5744.89 1.06656
1783 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Squared 13244.1 14564.4 1.09969
actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391] Measured 5386.37 5744.89 1.06656
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Rooted 67.1494 69.2625 1.03147
homeobox protein meis1. [swissprot;acc:o00470] Ranked 206.332 203.874 1.01206
1784 40s ribosomal protein s16. [swissprot;acc:p17008] Squared 13244.1 14564.4 1.09969
arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145] Measured 5386.37 5744.89 1.06656
beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Rooted 67.1494 69.2625 1.03147
homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] Ranked 206.332 203.874 1.01206
1785 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816]
nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847] Measured 5386.37 5744.89 1.06656
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Rooted 67.1523 69.2654 1.03147
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Squared 19340.3 21267.5 1.09965

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/