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 description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1980 to 2029 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
495 YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Subtracted High confidence 222.146 237.393 15.247
496 no value 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
PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] High confidence 250.938 234.134 1.07177
RNF113A zinc finger protein 183. [swissprot;acc:o15541] Subtracted Low confidence 205.192 198.726 6.466
497 CAPS calcyphosine. [swissprot;acc:q13938] 204.363 197.899 6.464
EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Divided High confidence 251.344 234.514 1.07177
SART1 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 225.026 209.798 15.228
SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided Low confidence 203.117 196.671 1.03278
498 ARHGEF6 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
KIFAP3 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845] Low confidence 203.117 196.671 1.03278
RCL1 rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Subtracted 203.85 197.403 6.447
TLX3 t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] High confidence 237.28 252.492 15.212
499 BARX1 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
LIMD1 lim domains containing 1. [refseq;acc:nm_014240] Low confidence 203.117 196.671 6.446
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Divided 203.167 196.732 1.03271
TPI1 triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] High confidence 231.496 248.048 1.0715
500 no value probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Subtracted Low confidence 203.117 196.671 6.446
ING2 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Divided High confidence 224.662 240.673 1.07127
OPN4 opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Subtracted 237.28 252.492 15.212
RCL1 rna 3'-terminal phosphate cyclase-like protein (hspc338). [swissprot;acc:q9y2p8] Divided Low confidence 203.85 197.403 1.03266
501 CAPS calcyphosine. [swissprot;acc:q13938] 204.363 197.899
CYC1 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] High confidence 238.704 255.68 1.07112
SF4 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Subtracted Low confidence 203.117 196.671 6.446
TLX2 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 ARHGAP26 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Divided 238.704 255.68 1.07112
KIFAP3 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845] Subtracted Low confidence 203.117 196.671 6.446
SART1 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] Divided 200.271 193.957 1.03255
TLX1 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 FOXO4 putative fork head domain transcription factor afx1 (forkhead box protein o4). [swissprot;acc:p98177] Low confidence 205.157 198.715 6.442
HECTD1 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8] High confidence 237.28 252.492 15.212
RGN senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Divided 238.704 255.68 1.07112
USP22 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 no value hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] Subtracted 205.157 198.715 6.442
BARX2 homeobox protein barh-like 2. [swissprot;acc:q9umq3] High confidence 237.28 252.492 15.212
OPHN1 oligophrenin 1. [swissprot;acc:o60890] Divided 238.704 255.68 1.07112
RNF113A zinc finger protein 183. [swissprot;acc:o15541] Low confidence 205.192 198.726 1.03254
505 APP amyloid beta a4 protein precursor (app) (abpp) (alzheimer's disease amyloid protein) (cerebral vascular amyloid peptide) (cvap) (protease nexin-ii) (pn-ii) (appi) (prea4) [contains: soluble app-alpha (s-app- alpha); soluble app-beta (s-app-beta); c99; beta-amyloid protein 42 (beta-app42); beta-amyloid protein 40 (beta-app40); c83; p3(42); p3(40); gamma-ctf(59) (gamma-secretase c-terminal fragment 59) (amyloid intracellular domain 59) (aid(59)); gamma-ctf(57) (gamma- secretase c-terminal fragment 57) (amyloid intracellular domain 57) (aid(57)); gamma-ctf(50) (gamma-secretase c-terminal fragment 50) (amyloid intracellular domain 50) (aid(50)); c31]. [swissprot;acc:p05067] Subtracted 205.157 198.715 6.442
NOC3L ad24 protein. [refseq;acc:nm_022451] Divided High confidence 251.334 234.672 1.071
PCNA proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] Low confidence 207.84 201.297 1.0325
ZNF593 zinc finger protein t86. [swissprot;acc:o00488] Subtracted High confidence 246.805 231.796 15.009
506 EXOSC4 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 215.237 230.07 14.833
FOXO4 putative fork head domain transcription factor afx1 (forkhead box protein o4). [swissprot;acc:p98177] Divided Low confidence 205.157 198.715 1.03242
ING1 inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] High confidence 224.535 240.476 1.071
TTYH2 tweety homolog 2. [refseq;acc:nm_032646] Subtracted Low confidence 205.157 198.715 6.442
507 no value hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] Divided 1.03242
EXOSC2 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Subtracted High confidence 215.237 230.07 14.833
HBZ hemoglobin zeta chain (hbaz). [swissprot;acc:p02008] Low confidence 205.157 198.715 6.442
WDR12 wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Divided High confidence 251.299 234.729 1.07059
508 no value alpha 2 globin. [refseq;acc:nm_000517] Subtracted Low confidence 205.157 198.715 6.442

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/