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 958 to 1007 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
479 protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79] Low confidence 207.68 214.591 1.03328
480 neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092] High confidence 237.109 254.667 1.07405
ns1-associated protein 1. [refseq;acc:nm_006372] Low confidence 203.822 197.259 1.03327
481 neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966] High confidence 237.109 254.667 1.07405
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Low confidence 171.564 166.045 1.03324
482 heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839] High confidence 237.109 254.667 1.07405
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Low confidence 204.65 198.086 1.03314
483 rna-binding protein. [refseq;acc:nm_019027] 203.821 197.289 1.03311
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] High confidence 237.109 254.667 1.07405
484 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Low confidence 203.821 197.291 1.0331
e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] High confidence 237.109 254.667 1.07405
485 60s ribosomal protein l18. [swissprot;acc:q07020]
tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Low confidence 205.109 198.551 1.03303
486 chromosome x open reading frame 9; likely ortholog of mouse sh3 gene sly. [refseq;acc:nm_018990] 204.331 211.075 1.03301
mct-1 protein. [refseq;acc:nm_014060] High confidence 226.313 243.03 1.07387
487 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Low confidence 206.763 200.18 1.03289
488 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9] 209.136 202.478 1.03288
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] High confidence 225.026 209.798 1.07258
489 protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 231.276 215.627 1.07257
ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9] Low confidence 209.136 202.478 1.03288
490 rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] High confidence 220.183 236.015 1.0719
tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289] Low confidence 209.136 202.478 1.03288
491 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] High confidence 251.83 234.951 1.07184
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Low confidence 209.136 202.478 1.03288
492 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] High confidence 220.171 235.979 1.0718
493 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Low confidence 209.136 202.478 1.03288
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] High confidence 220.172 235.98 1.0718
494 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Low confidence 206.154 199.596 1.03286
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] High confidence 220.172 235.98 1.0718
495 lim domains containing 1. [refseq;acc:nm_014240] Low confidence 203.117 196.671 1.03278
serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] High confidence 220.171 235.979 1.0718
496 probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Low confidence 203.117 196.671 1.03278
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] High confidence 250.938 234.134 1.07177
497 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 251.344 234.514
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Low confidence 203.117 196.671 1.03278
498 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845]
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] High confidence 220.161 235.95 1.07172
499 polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Low confidence 203.167 196.732 1.03271
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] High confidence 231.496 248.048 1.0715
500 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 224.662 240.673 1.07127
rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Low confidence 203.85 197.403 1.03266
501 calcyphosine. [swissprot;acc:q13938] 204.363 197.899
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] High confidence 238.704 255.68 1.07112
502 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Low confidence 200.271 193.957 1.03255
503 senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] High confidence 238.704 255.68 1.07112
ubiquitin carboxyl-terminal hydrolase 22 (ec 3.1.2.15) (ubiquitin thiolesterase 22) (ubiquitin-specific processing protease 22) (deubiquitinating enzyme 22) (fragment). [swissprot;acc:q9upt9] Low confidence 207.407 200.869 1.03255
504 oligophrenin 1. [swissprot;acc:o60890] High confidence 238.704 255.68 1.07112

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/