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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1358 to 1407 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
red
green
network_comparison
679 sorting nexin 5. [swissprot;acc:q9y5x3] SNX5 Subtracted 208.482 220.175 11.693
680 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] HOXB4 Divided 132.413 125.389 1.05602
sr rich protein. [refseq;acc:nm_032870] SFRS18 Subtracted 225.293 213.64 11.653
681 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] HOXC5 Divided 132.413 125.389 1.05602
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] SNW1 Subtracted 220.593 208.987 11.606
682 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Divided 132.413 125.389 1.05602
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] NAT10 Subtracted 246.055 234.458 11.597
683 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Divided 132.413 125.389 1.05602
osteoclast stimulating factor 1. [swissprot;acc:q92882] OSTF1 Subtracted 231.809 243.289 11.48
684 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Divided 132.413 125.389 1.05602
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] PFAS Subtracted 223.58 235.027 11.447
685 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] ATIC
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Divided 132.413 125.389 1.05602
686 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] PAICS Subtracted 223.58 235.027 11.447
687 dendritic cell protein. [refseq;acc:nm_006360] EIF3M 223.121 211.685 11.436
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Divided 132.413 125.389 1.05602
688 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] POLR2D 237.554 250.823 1.05586
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] CPXM2 Subtracted 223.121 211.685 11.436
689 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] CPN1
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] TCP1 Divided 135.379 128.225 1.05579
690 cpz gene product. [refseq;acc:nm_003652] CPZ Subtracted 223.121 211.685 11.436
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] SNW1 Divided 220.593 208.987 1.05553
691 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] BCAS2 217.602 206.195 1.05532
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] CPE Subtracted 223.121 211.685 11.436
692 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] CDC5L Divided 217.602 206.195 1.05532
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] CPXM1 Subtracted 223.121 211.685 11.436
693 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] BCAS2 217.602 206.195 11.407
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] NOVA1 Divided 222.554 234.847 1.05524
694 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] CDC5L Subtracted 217.602 206.195 11.407
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] POLE Divided 241.907 229.35 1.05475
695 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] NUBP1 Subtracted 210.739 199.398 11.341
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] PPIL4 Divided 226.135 214.405 1.05471
696 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] NUBP2 Subtracted 210.739 199.398 11.341
sr rich protein. [refseq;acc:nm_032870] SFRS18 Divided 225.293 213.64 1.05455
697 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] FTH1 220.444 209.113 1.05419
Subtracted 11.331
698 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] CREG2 220.438 209.118 11.32
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] FTMT Divided 220.437 1.05413
699 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] CREG2 220.438
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] no value Subtracted 11.32
700 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] DLGAP1
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] no value Divided 1.05413
701 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] DLGAP1
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] AHCYL1 Subtracted 11.32
702 limkain b1. [refseq;acc:nm_019081] KIAA0430
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] AHCYL1 Divided 1.05413
703 limkain b1. [refseq;acc:nm_019081] KIAA0430
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] no value Subtracted 11.32
704 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] CREG1

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/