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 6358 to 6407 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1590 prefoldin subunit 1. [swissprot;acc:o60925] Subtracted High confidence 5875.75 6302.76 427.01
ras-related protein rab-5b. [swissprot;acc:p35239] Divided Low confidence 7969.92 8238.53 1.0337
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Subtracted 8105.19 8373.45 268.26
1591 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Divided High confidence 6364.01 6819.38 1.07155
n-glycanase 1. [refseq;acc:nm_018297] Subtracted Low confidence 8001.38 8269.55 268.17
secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138] High confidence 5875.75 6302.76 427.01
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Divided Low confidence 7782.52 8044.76 1.0337
1592 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] High confidence 5853.1 6271.79 1.07153
choline dehydrogenase. [refseq;acc:nm_018397] Subtracted 5875.75 6302.76 427.01
ptk9 protein tyrosine kinase 9; protein tyrosine kinase 9. [refseq;acc:nm_002822] Low confidence 8114.25 8382.4 268.15
serine/threonine kinase 38 like. [refseq;acc:nm_015000] Divided 8152.52 8427.18 1.03369
1593 colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Subtracted High confidence 6520.83 6946.75 425.92
proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Divided 4977.77 5333.78 1.07152
ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907] Subtracted Low confidence 7867.46 8135.55 268.09
stress-70 protein, mitochondrial precursor (75 kda glucose regulated protein) (grp 75) (peptide-binding protein 74) (pbp74) (mortalin) (mot). [swissprot;acc:p38646] Divided 8068.55 8340.4 1.03369
1594 atp-dependent dna helicase q1 (dna-dependent atpase q1). [swissprot;acc:p46063] 8147.51 8421.91 1.03368
glycine dehydrogenase [decarboxylating], mitochondrial precursor (ec 1.4.4.2) (glycine decarboxylase) (glycine cleavage system p- protein). [swissprot;acc:p23378] Subtracted High confidence 5933.25 6358.78 425.53
proprotein convertase subtilisin/kexin type 9 preproprotein; neural apoptosis regulated convertase 1; hypercholesterolemia, autosomal dominant 3. [refseq;acc:nm_174936] Low confidence 7973.26 8241.35 268.09
transportin-sr; importin 12. [refseq;acc:nm_012470] Divided High confidence 5184.94 5555.76 1.07152
1595 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Low confidence 8549.01 8270.52 1.03367
dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Subtracted High confidence 3760.3 4185.82 425.52
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] Divided 6351.32 6805.39 1.07149
ptk9l protein tyrosine kinase 9-like (a6-related protein); protein tyrosine kinase 9-like (a6-related protein). [refseq;acc:nm_007284] Subtracted Low confidence 8113.81 8381.9 268.09
1596 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] High confidence 5659.22 6084.68 425.46
enigma protein; lim domain protein. [refseq;acc:nm_005451] Divided 5665.34 6070.32 1.07148
spermatogenesis associated factor spaf. [refseq;acc:nm_145207] Low confidence 7913.23 8179.69 1.03367
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Subtracted 7994.88 8262.97 268.09
1597 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] High confidence 6038.46 6463.9 425.44
eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] Divided 5665.34 6070.32 1.07148
probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1] Subtracted Low confidence 7610.71 7878.8 268.09
ras-related protein rab-5c (rab5l) (l1880). [swissprot;acc:p51148] Divided 7969.65 8238.02 1.03367
1598 kunitz-type protease inhibitor 2 precursor (hepatocyte growth factor activator inhibitor type 2) (hai-2) (placental bikunin). [swissprot;acc:o43291] Subtracted 7991.83 8259.89 268.06
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Divided High confidence 5068.17 5430.41 1.07147
mitochondrial ribosomal protein l30 isoform a. [refseq;acc:nm_145212] Subtracted 5923.66 6349.04 425.38
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Divided Low confidence 7961.17 8229.2 1.03367
1599 26s protease regulatory subunit s10b (proteasome subunit p42) (p44) (conserved atpase domain protein 44) (cadp44). [swissprot;acc:q92524] Subtracted High confidence 5923.66 6349.04 425.38
40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Divided 5184.45 5554.97 1.07147
dok-like protein. [refseq;acc:nm_024872] Low confidence 7889.23 8154.7 1.03365
kunitz-type protease inhibitor 1 precursor (hepatocyte growth factor activator inhibitor type 1) (hai-1). [swissprot;acc:o43278] Subtracted 7991.83 8259.89 268.06
1600 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] Divided High confidence 6336.22 6788.96 1.07145
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Low confidence 7889.23 8154.7 1.03365
er-resident protein erdj5; macrothioredoxin; j-domain-containing protein disulfide isomerase-like protein. [refseq;acc:nm_018981] Subtracted 7991.83 8259.89 268.06
wd-repeat protein bing4. [swissprot;acc:o15213] High confidence 4066.56 4491.65 425.09
1601 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 5660.17 6085.22 425.05
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Divided Low confidence 7889.23 8154.7 1.03365
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] High confidence 5232.14 5605.8 1.07142
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Subtracted Low confidence 7961.17 8229.2 268.03
1602 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] High confidence 5819.39 6244.37 424.98
dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889] Low confidence 8096.76 8364.77 268.01
mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] Divided 8049.75 8320.53 1.03364

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/