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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Gene Rank description Filtered Value Type Network Comparison Type green Interaction Map red network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
description
Filtered
green
Interaction Map
red
network_comparison
126 calcyphosine. [swissprot;acc:q13938] 0 635.875 High confidence 472.524 1.3457
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1 18164.9 24250 1.33499
fos-related antigen 2. [swissprot;acc:p15408] 0 2407.27 Low confidence 3205.98 1.33179
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 1 10318.5 11285.3 1.0937
127 lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 0 64 High confidence 86 1.34375
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 1 10318.5 Low confidence 11285.3 1.0937
transcription factor jun-d. [swissprot;acc:p17535] 7523.39 High confidence 5638.2 1.33436
ubiquinol-cytochrome c reductase complex 7.2 kda protein (ec 1.10.2.2) (cytochrome c1, nonheme 7 kda protein) (complex iii subunit x) (7.2 kda cytochrome c1-associated protein subunit) (hspc119). [swissprot;acc:q9udw1] 0 511.5 Low confidence 680.5 1.3304
128 double-stranded rna-specific editase 1 (ec 3.5.-.-) (dsrna adenosine deaminase) (rna editing deaminase 1) (rna editing enzyme 1). [swissprot;acc:p78563] 391 294 1.32993
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 1 5810.82 High confidence 4355.61 1.3341
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 10318.5 Low confidence 11285.3 1.0937
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 0 60.8613 High confidence 81.504 1.33918
129 amiloride-sensitive sodium channel delta-subunit (epithelial na+ channel delta subunit) (delta enac) (nonvoltage-gated sodium channel 1 delta subunit) (scned) (delta nach). [swissprot;acc:p51172] 194.326 Low confidence 146.219 1.32901
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 1 5811.49 High confidence 4358.13 1.33348
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 10318.5 Low confidence 11285.3 1.0937
protein hspc134 (protein cda04). [swissprot;acc:q9by43] 0 454.837 High confidence 606.485 1.33341
130 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 1 2978.53 2234.68 1.33287
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 0 56 42 1.33333
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] 1 10318.5 Low confidence 11285.3 1.0937
phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356] 0 937.501 707.801 1.32453
131 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 851.77 645.504 1.31954
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 1 2978.57 High confidence 2234.73 1.33285
serpin b11. [swissprot;acc:q96p15] 0 56 42 1.33333
trophinin. [swissprot;acc:q12816] 1 10318.5 Low confidence 11285.3 1.0937
132 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 0 56 High confidence 42 1.33333
dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] 1 5441.83 Low confidence 5948.88 1.09318
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 2980.35 High confidence 2236.61 1.33253
wd-repeat protein 5 (wd-repeat protein big-3). [swissprot;acc:q9ugp9] 0 191.971 Low confidence 251.947 1.31242
133 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 335 High confidence 252 1.32937
cdc42-binding protein kinase beta; cdc42-binding protein kinase beta (dmpk-like); mrck beta; dmpk-like. [refseq;acc:nm_006035] 1139 Low confidence 874 1.3032
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 1 17580.4 High confidence 23421.5 1.33225
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 7662.77 Low confidence 7013 1.09265
134 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 7286.66 6670.21 1.09242
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 16426.1 High confidence 21785.2 1.32626
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 0 346.751 260.986 1.32862
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 1139 Low confidence 874 1.3032
135 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 1 16426.1 High confidence 21785.2 1.32626
high-mobility group 20a. [refseq;acc:nm_018200] 7916.96 Low confidence 7248.24 1.09226
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 0 203.832 265.513 1.30261
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] 613.614 High confidence 814.485 1.32736
136 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 154.324 Low confidence 200.834 1.30138
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] 1 4763.34 High confidence 3620.77 1.31556
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] 7667.34 Low confidence 7020.48 1.09214
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 0 1150.51 High confidence 1526.38 1.3267
137 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] 154.279 Low confidence 200.759 1.30127
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 1 4763.34 High confidence 3620.77 1.31556
heat shock factor binding protein 1. [swissprot;acc:o75506] 0 1233.41 1631.18 1.3225
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] 1 6699.58 Low confidence 6139.6 1.09121
138 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 0 154.279 200.759 1.30127
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 1 7313.38 6709 1.09008

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/