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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3941 to 3990 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
red
green
network_comparison
493 MICAL2 Measured flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Subtracted 6167.93 7007.7 839.77
NAV3 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Divided 5979.95 6842.78 1.14429
VAMP3 Squared vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Subtracted 27516.2 32720 5203.8
ZNRD1 Ranked zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] 236.751 252.038 15.287
494 ANKS1B Measured e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Divided 5979.93 6842.72 1.14428
ETFA Squared electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] 31583 37925.6 1.20082
GNL3 Rooted nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Subtracted 49.3771 54.5905 5.2134
INPP4B Measured inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] 6167.93 7007.7 839.77
MTX2 Ranked metaxin 2. [swissprot;acc:o75431] 219.537 234.793 15.256
PAK1 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
PSIP1 Rooted pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] 55.1759 60.2621 1.09218
RBL1 Squared retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Subtracted 29174 34363.5 5189.5
495 CLEC3B Measured tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Divided 10804.7 12363.6 1.14428
PAK3 Ranked serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 220.171 235.979 1.0718
PARD6G Squared partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 30286.5 36362 1.2006
PROSC Rooted proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Subtracted 68.6822 73.8955 5.2133
RBL2 Squared retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 29173.8 34362.7 5188.9
RPL8 Rooted 60s ribosomal protein l8. [swissprot;acc:p25120] Divided 55.1759 60.2621 1.09218
SEPHS1 Measured selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Subtracted 6167.93 7007.7 839.77
YME1L1 Ranked yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] 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
ATP5D Squared atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 27162.5 32347.5 5185
HDGF Rooted hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Divided 55.1759 60.2621 1.09218
INPP4A Measured inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Subtracted 6167.93 7007.7 839.77
NOSTRIN nostrin. [refseq;acc:nm_052946] Divided 4682.87 4093.05 1.1441
PES1 Rooted pescadillo homolog 1. [swissprot;acc:o00541] Subtracted 49.2488 54.4603 5.2115
PPAN-P2RY11 Ranked suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Divided 250.938 234.134 1.07177
TUB Squared tubby protein homolog. [swissprot;acc:p50607] 30286.5 36362 1.2006
497 CDYL2 chromodomain y-like protein 2. [refseq;acc:nm_152342] Subtracted 29016.1 34169.2 5153.1
DHX15 Measured putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 4714.85 5554.38 839.53
EBNA1BP2 Ranked probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Divided 251.344 234.514 1.07177
HDGFL1 Rooted pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] 55.1759 60.2621 1.09218
PRKCI Squared protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] 30286.5 36362 1.2006
SART1 Ranked 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
SIN3A Rooted transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] 50.4687 45.2733 5.1954
SNF8 Measured eap30 subunit of ell complex. [refseq;acc:nm_007241] Divided 4682.87 4093.05 1.1441
498 ARHGEF6 Ranked rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] 220.161 235.95 1.07172
BTF3 Measured transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Subtracted 6933.17 7766.54 833.37
CDY1B Squared testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 29012.2 34163.9 5151.7
DDX6 Rooted probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Divided 55.1759 60.2621 1.09218
DENR density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Subtracted 50.4687 45.2733 5.1954
NUMB Squared numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Divided 30286.5 36362 1.2006
SLC39A6 Measured liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 4682.87 4093.05 1.1441
TLX3 Ranked t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Subtracted 237.28 252.492 15.212
499 no value Measured transcription factor btf3 homolog 3. [swissprot;acc:q13892] 6938.22 7770.65 832.43
BARX1 Ranked homeobox protein barh-like 1. [swissprot;acc:q9hbu1] 237.28 252.492 15.212
CDYL Squared chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] 29012.2 34163.9 5151.7
GAD2 Measured glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Divided 4682.87 4093.05 1.1441
NOL1 Rooted proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Subtracted 49.7541 54.9425 5.1884
TBC1D5 Squared tbc1 domain family member 5. [swissprot;acc:q92609] Divided 30286.5 36362 1.2006

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/