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 1963 to 2012 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
491 rna-binding protein. [refseq;acc:nm_019027] Subtracted Low confidence 203.821 197.289 6.532
sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1] Divided 209.136 202.478 1.03288
492 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Subtracted 203.821 197.291 6.53
beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] High confidence 150.982 166.372 15.39
neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1] Divided Low confidence 209.136 202.478 1.03288
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
tissue alpha-l-fucosidase precursor (ec 3.2.1.51) (alpha-l-fucosidase i) (alpha-l-fucoside fucohydrolase). [swissprot;acc:p04066] Subtracted Low confidence 202.271 195.742 6.529
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] High confidence 236.751 252.038 15.287
494 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Divided Low confidence 206.154 199.596 1.03286
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Subtracted 208.004 201.497 6.507
metaxin 2. [swissprot;acc:o75431] High confidence 219.537 234.793 15.256
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Divided 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
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Subtracted Low confidence 198.464 191.96 6.504
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] High confidence 222.146 237.393 15.247
496 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 250.419 15.239
probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Divided 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
zinc finger protein 183. [swissprot;acc:o15541] Subtracted Low confidence 205.192 198.726 6.466
497 calcyphosine. [swissprot;acc:q13938] 204.363 197.899 6.464
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Divided High confidence 251.344 234.514 1.07177
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Low confidence 203.117 196.671 1.03278
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] Subtracted High confidence 225.026 209.798 15.228
498 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845] Divided Low confidence 203.117 196.671 1.03278
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
rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Subtracted Low confidence 203.85 197.403 6.447
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] High confidence 237.28 252.492 15.212
499 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
lim domains containing 1. [refseq;acc:nm_014240] Low confidence 203.117 196.671 6.446
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Divided 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
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Subtracted 237.28 252.492 15.212
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 6.446
rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Divided 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
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Subtracted Low confidence 203.117 196.671 6.446
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] High confidence 237.28 252.492 15.212
502 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845] Low confidence 203.117 196.671 6.446
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Divided High confidence 238.704 255.68 1.07112
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
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Subtracted High confidence 237.28 252.492 15.212
503 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
putative fork head domain transcription factor afx1 (forkhead box protein o4). [swissprot;acc:p98177] Low confidence 205.157 198.715 6.442
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Divided 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

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/