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 Network Comparison Type Hugo description Value Type Interaction Map Filtered network_comparison red green
Results: HTML CSV LaTeX Showing element 5591 to 5640 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
network_comparison
red
green
2796 Divided DMAP1 dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5] 1 0.00001 0.00001
Subtracted 0 0 0
2797 Divided ODF3 sperm tail protein shippo1; h-shippo 1. [refseq;acc:nm_053280] 1 0.00001 0.00001
Subtracted 0 0 0
2798 Divided ARIH2 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 1 0.00001 0.00001
Subtracted 0 0 0
2799 Divided HMGB4 hmg2 like. [refseq;acc:nm_145205] 1 0.00001 0.00001
Subtracted 0 0 0
2800 Divided MLXIP mondoa. [refseq;acc:nm_014938] 1 0.00001 0.00001
Subtracted 0 0 0
2801 Divided ERCC4 dna-repair protein complementing xp-f cell (xeroderma pigmentosum group f complementing protein) (dna excision repair protein ercc-4). [swissprot;acc:q92889] 1 0.00001 0.00001
Subtracted 0 0 0
2802 Divided no value 3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] 1 0.00001 0.00001
Subtracted 0 0 0
2803 Divided nanos (fragment). [sptrembl;acc:q8wy41] 1 0.00001 0.00001
Subtracted 0 0 0
2804 Divided BANF1 barrier-to-autointegration factor (breakpoint cluster region protein 1). [swissprot;acc:o75531] 1 0.00001 0.00001
Subtracted 0 0 0
2805 Divided PACS1 phosphofurin acidic cluster sorting protein 1 isoform 1; cytosolic sorting protein pacs-1. [refseq;acc:nm_018026] 1 0.00001 0.00001
Subtracted 0 0 0
2806 Divided SPSB4 spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862] 1 0.00001 0.00001
Subtracted 0 0 0
2807 Divided RAB1C ras-related protein rab-1b. [swissprot;acc:q9h0u4] 1 0.00001 0.00001
Subtracted 0 0 0
2808 Divided LIG4 dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917] 1 0.00001 0.00001
Subtracted 0 0 0
2809 Divided PHC3 polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947] 1 0.00001 0.00001
Subtracted 0 0 0
2810 Divided UGT2A1 udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798] 1 0.00001 0.00001
Subtracted 0 0 0
2811 Divided VEGFB vascular endothelial growth factor b precursor (vegf-b) (vegf related factor) (vrf). [swissprot;acc:p49765] 1 0.00001 0.00001
Subtracted 0 0 0
2812 Divided MOBKL2A mob-lak. [refseq;acc:nm_130807] 1 0.00001 0.00001
Subtracted 0 0 0
2813 Divided HDAC3 histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379] 1 0.00001 0.00001
Subtracted 0 0 0
2814 Divided SPSB1 spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106] 1 0.00001 0.00001
Subtracted 0 0 0
2815 Divided NMUR1 g protein-coupled receptor 66. [refseq;acc:nm_006056] 1 0.00001 0.00001
Subtracted 0 0 0
2816 Divided TIGD1 tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] 1 0.00001 0.00001
Subtracted 0 0 0
2817 Divided TBCA tubulin-specific chaperone a (tubulin-folding cofactor a) (cfa) (tcp1-chaperonin cofactor a). [swissprot;acc:o75347] 1 0.00001 0.00001
Subtracted 0 0 0
2818 Divided UGT2B7 udp-glucuronosyltransferase 2b7 precursor, microsomal (ec 2.4.1.17) (udpgt) (3,4-catechol estrogen specific) (udpgth-2). [swissprot;acc:p16662] 1 0.00001 0.00001
Subtracted 0 0 0
2819 Divided no value udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 1 0.00001 0.00001
Subtracted 0 0 0
2820 Divided peregrin (bromodomain and phd finger-containing protein 1) (br140 protein). [swissprot;acc:p55201] 1 0.00001 0.00001
Subtracted 0 0 0

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/