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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 700 to 749 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
175 PANK2 Rooted pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 145.551 168.796 1.1597
176 MXD4 Measured max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 4456.93 5773.67 1.29544
PANK3 Rooted pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] 145.551 168.796 1.1597
POLE4 Ranked dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 275.754 235.908 1.1689
TRAPPC3 Squared bet3 homolog. [swissprot;acc:o43617] 112820 157033 1.39189
177 NCBP2L Ranked dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 229.406 196.695 1.1663
RAB24 Measured max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 4457.06 5773.63 1.29539
SEPT1 Squared septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 78383 108483 1.38401
SLC25A43 Rooted mitochondrial solute carrier protein. [refseq;acc:nm_145305] 145.551 168.796 1.1597
178 no value Ranked formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 226.887 194.72 1.1652
CPA6 Squared carboxypeptidase b precursor. [refseq;acc:nm_020361] 25326.4 18354.1 1.37988
MYO5B Measured myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] 21591.5 27904.5 1.29238
TFDP2 Rooted transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 45.7414 52.932 1.1572
179 no value Ranked huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 226.884 194.79 1.16476
CPA3 Squared mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 25326.3 18354.1 1.37987
EGFL8 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
MYO5C Measured myosin vc (myosin 5c). [swissprot;acc:q9nqx4] 21591.5 27904.5 1.29238
180 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
CPB2 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
EGFL7 Rooted egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] 50.2801 43.4779 1.15645
TARDBP Ranked tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 256.228 298.438 1.16474
181 B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 1.16294
BCAR1 Rooted crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 57.4432 66.3307 1.15472
EIF4G3 Measured eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 4068.56 5252.6 1.29102
NFU1 Squared hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 55630.4 76083.7 1.36766
182 no value Measured rna-binding protein. [refseq;acc:nm_019027] 4069.83 5252.17 1.29051
CCT4 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
DUT Squared deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 61733.5 45224.1 1.36506
HAT1 Ranked histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 277.546 240.461 1.15422
183 no value 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
ACADVL Squared acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 79779.8 108084 1.35478
NCBP2 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
NEDD9 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 no value Squared small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 72886.3 98544.5 1.35203
ATG4A 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
OSR1 Ranked odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 274.027 237.79 1.15239
SYNCRIP Measured ns1-associated protein 1. [refseq;acc:nm_006372] 4069.83 5252.17 1.29051
185 ADIPOR2 Ranked adiponectin receptor 2. [refseq;acc:nm_024551] 281.582 246.371 1.14292
HNRNPR Measured heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 4069.83 5252.17 1.29051
HS3ST6 Squared c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 41502.9 30836.8 1.34589
MAP1LC3B 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 EIF4G1 Measured eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 4071.1 5251.75 1.29001
FLNB 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
HS3ST3A1 Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 41502.9 30836.8 1.34589
MAP1LC3A 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 ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 153.548 133.153 1.15317
HS3ST3B1 Squared heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 41502.9 30836.8 1.34589
REV1 Ranked rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 226.582 198.444 1.14179
SNRPD3 Measured small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 4569.48 5885.79 1.28807
188 E2F1 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

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
- Hugo is the HGNC identifier if it exists
- 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/