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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank description Value Type Network Comparison Type Filtered Interaction Map network_comparison green red
Results: HTML CSV LaTeX Showing element 501 to 550 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
Rank
description
Filtered
Interaction Map
network_comparison
green
red
126 calcyphosine. [swissprot;acc:q13938] 0 High confidence 1.3457 635.875 472.524
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 1 1.33499 18164.9 24250
fos-related antigen 2. [swissprot;acc:p15408] 0 Low confidence 1.33179 2407.27 3205.98
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 1 1.0937 10318.5 11285.3
127 lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 0 High confidence 1.34375 64 86
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 1 Low confidence 1.0937 10318.5 11285.3
transcription factor jun-d. [swissprot;acc:p17535] High confidence 1.33436 7523.39 5638.2
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 Low confidence 1.3304 511.5 680.5
128 double-stranded rna-specific editase 1 (ec 3.5.-.-) (dsrna adenosine deaminase) (rna editing deaminase 1) (rna editing enzyme 1). [swissprot;acc:p78563] 1.32993 391 294
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 1 High confidence 1.3341 5810.82 4355.61
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] Low confidence 1.0937 10318.5 11285.3
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 0 High confidence 1.33918 60.8613 81.504
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] Low confidence 1.32901 194.326 146.219
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 1 High confidence 1.33348 5811.49 4358.13
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] Low confidence 1.0937 10318.5 11285.3
protein hspc134 (protein cda04). [swissprot;acc:q9by43] 0 High confidence 1.33341 454.837 606.485
130 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 1 1.33287 2978.53 2234.68
maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 0 1.33333 56 42
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 Low confidence 1.0937 10318.5 11285.3
phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356] 0 1.32453 937.501 707.801
131 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 1.31954 851.77 645.504
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] 1 High confidence 1.33285 2978.57 2234.73
serpin b11. [swissprot;acc:q96p15] 0 1.33333 56 42
trophinin. [swissprot;acc:q12816] 1 Low confidence 1.0937 10318.5 11285.3
132 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 0 High confidence 1.33333 56 42
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 Low confidence 1.09318 5441.83 5948.88
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] High confidence 1.33253 2980.35 2236.61
wd-repeat protein 5 (wd-repeat protein big-3). [swissprot;acc:q9ugp9] 0 Low confidence 1.31242 191.971 251.947
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] High confidence 1.32937 335 252
cdc42-binding protein kinase beta; cdc42-binding protein kinase beta (dmpk-like); mrck beta; dmpk-like. [refseq;acc:nm_006035] Low confidence 1.3032 1139 874
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 1 High confidence 1.33225 17580.4 23421.5
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Low confidence 1.09265 7662.77 7013
134 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] 1.09242 7286.66 6670.21
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] High confidence 1.32626 16426.1 21785.2
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 0 1.32862 346.751 260.986
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Low confidence 1.3032 1139 874
135 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 1 High confidence 1.32626 16426.1 21785.2
high-mobility group 20a. [refseq;acc:nm_018200] Low confidence 1.09226 7916.96 7248.24
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 0 1.30261 203.832 265.513
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] High confidence 1.32736 613.614 814.485
136 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Low confidence 1.30138 154.324 200.834
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 High confidence 1.31556 4763.34 3620.77
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Low confidence 1.09214 7667.34 7020.48
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 0 High confidence 1.3267 1150.51 1526.38
137 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Low confidence 1.30127 154.279 200.759
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 High confidence 1.31556 4763.34 3620.77
heat shock factor binding protein 1. [swissprot;acc:o75506] 0 1.3225 1233.41 1631.18
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] 1 Low confidence 1.09121 6699.58 6139.6
138 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 0 1.30127 154.279 200.759
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 1 1.09008 7313.38 6709

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/