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 [...,...].
Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 712 to 761 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
178 Rooted transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 45.7414 52.932 1.1572
179 Measured myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 21591.5 27904.5 1.29238
Ranked huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 226.884 194.79 1.16476
Squared mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 25326.3 18354.1 1.37987
Rooted palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5] 50.272 43.4634 1.15665
180 Measured myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] 21591.5 27904.5 1.29238
Ranked tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 256.228 298.438 1.16474
Squared plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 25326.2 18354.1 1.37987
Rooted egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 50.2801 43.4779 1.15645
181 Measured eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 4068.56 5252.6 1.29102
Ranked b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 1.16294
Squared hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 55630.4 76083.7 1.36766
Rooted crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 57.4432 66.3307 1.15472
182 Measured rna-binding protein. [refseq;acc:nm_019027] 4069.83 5252.17 1.29051
Ranked histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 277.546 240.461 1.15422
Squared deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 61733.5 45224.1 1.36506
Rooted t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 57.45 66.332 1.1546
183 Measured apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 4069.83 5252.17 1.29051
Ranked 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 228.306 198.011 1.153
Squared acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 79779.8 108084 1.35478
Rooted enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 57.4586 66.3336 1.15446
184 Measured ns1-associated protein 1. [refseq;acc:nm_006372] 4069.83 5252.17 1.29051
Ranked odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 274.027 237.79 1.15239
Squared small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 72886.3 98544.5 1.35203
Rooted cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 153.602 133.195 1.15321
185 Measured heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 4069.83 5252.17 1.29051
Ranked adiponectin receptor 2. [refseq;acc:nm_024551] 281.582 246.371 1.14292
Squared c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 41502.9 30836.8 1.34589
Rooted microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] 153.578 133.176 1.1532
186 Measured eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 4071.1 5251.75 1.29001
Ranked filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 226.582 198.444 1.14179
Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 41502.9 30836.8 1.34589
Rooted microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] 153.578 133.176 1.1532
187 Measured small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 4569.48 5885.79 1.28807
Ranked rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 226.582 198.444 1.14179
Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 41502.9 30836.8 1.34589
Rooted cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 153.548 133.153 1.15317
188 Measured source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 4571.89 5864.86 1.28281
Ranked protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 226.582 198.444 1.14179
Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 41502.9 30836.8 1.34589
Rooted transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] 46.0352 53.0192 1.15171
189 Measured oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 4571.89 5864.86 1.28281
Ranked protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 226.582 198.444 1.14179
Squared mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 41502.9 30836.8 1.34589
Rooted transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 46.0352 53.0192 1.15171
190 Measured dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 4571.89 5864.86 1.28281
Ranked u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 226.582 198.444 1.14179
Squared aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 71389.9 96037.6 1.34525
Rooted gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 149.165 129.699 1.15009
191 Measured splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 4638.1 5923.4 1.27712

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/