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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Hugo Rank Gene description measured expected final
Results: HTML CSV LaTeX Showing element 2002 to 2051 of 3206 in total
Hugo
Rank
description
measured
expected
final
NLK 1701 NEMO-LIKE KINASE; LIKELY ORTHOLOG OF MOUSE NEMO LIKE KINASE. [RefSeq;Acc:NM_016231] 0.210207 0.883788 0.237847764
NME2 2010 NUCLEOSIDE DIPHOSPHATE KINASE A (EC 2.7.4.6) (NDK A) (NDP KINASE A) (TUMOR METASTATIC PROCESS-ASSOCIATED PROTEIN) (METASTASIS INHIBITION FACTOR NM23) (NM23-H1). [SWISSPROT;Acc:P15531] 0.494361 2.14316 0.230669199
NME2P1 2011 PUTATIVE NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) (NDK) (NDP KINASE). [SWISSPROT;Acc:O60361] 0.480816 2.08449 0.230663616
NME3 2065 NUCLEOSIDE DIPHOSPHATE KINASE 3 (EC 2.7.4.6) (NDK 3) (NDP KINASE 3) (NM23-H3) (DR-NM23). [SWISSPROT;Acc:Q13232] 0.366443 1.59695 0.229464291
NMNAT3 1682 NICOTINAMIDE NUCLEOTIDE ADENYLYLTRANSFERASE 3; PYRIDINE NUCLEOTIDE ADENYLYLTRANSFERASE 3. [RefSeq;Acc:NM_178177] 0.192536 0.808409 0.238166572
NOB1 1532 NIN ONE BINDING PROTEIN; ADENOCARCINOMA ANTIGEN RECOGNIZED BY T LYMPHOCYTES 4. [RefSeq;Acc:NM_014062] 0.0805704 0.332683 0.2421837
NOC3L 1334 AD24 PROTEIN. [RefSeq;Acc:NM_022451] 0.290237 1.18321 0.24529627
NOC4L 1507 0.511781 2.10953 0.242604277
NOL1 1565 PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120 (PROLIFERATION-ASSOCIATED NUCLEOLAR PROTEIN P120). [SWISSPROT;Acc:P46087] 0.714168 2.96197 0.241112503
NOL10 1416 0.651969 2.67215 0.243986677
NOL14 1483 0.54526 2.24437 0.242945682
NOL5A 1523 NUCLEOLAR PROTEIN NOP56 (NUCLEOLAR PROTEIN 5A). [SWISSPROT;Acc:O00567] 0.66215 2.73239 0.242333635
NOL6 1267 NUCLEOLAR RNA-ASSOCIATED PROTEIN ALPHA ISOFORM. [RefSeq;Acc:NM_022917] 0.966893 3.91912 0.246711762
NOLA1 256 "NUCLEOLAR PROTEIN FAMILY A, MEMBER 1; GAR1 PROTEIN. [RefSeq;Acc:NM_018983]" 0.11305 0.363171 0.311285868
NOLA2 1714 "NUCLEOLAR PROTEIN FAMILY A, MEMBER 2; COMPONENT OF THE H/ACA SNORNP. [RefSeq;Acc:NM_017838]" 0.0909039 0.382985 0.237356293
NONO 1676 "54 KDA NUCLEAR RNA- AND DNA-BINDING PROTEIN (P54(NRB)) (P54NRB) (55 KDA NUCLEAR PROTEIN) (NMT55) (NON-POU DOMAIN-CONTAINING OCTAMER- BINDING PROTEIN) (DNA-BINDING P52/P100 COMPLEX, 52 KDA SUBUNIT). [SWISSPROT;Acc:Q15233]" 0.201833 0.847008 0.238289367
NOSTRIN 1730 NOSTRIN. [RefSeq;Acc:NM_052946] 0.02137 0.0901539 0.237039108
NOVA1 1208 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] 0.107742 0.434244 0.248113964
NPC2 272 EPIDIDYMAL SECRETORY PROTEIN E1 PRECURSOR (NIEMANN-PICK DISEASE TYPE C2 PROTEIN) (EPI-1) (HE1) (EPIDIDYMAL SECRETORY PROTEIN 14.6) (ESP14.6). [SWISSPROT;Acc:Q15668] 0.115432 0.377878 0.305474254
NPEPPS 2270 PUROMYCIN-SENSITIVE AMINOPEPTIDASE (EC 3.4.11.-) (PSA). [SWISSPROT;Acc:P55786] 0.0267797 0.120229 0.222739106
NPLOC4 446 0.260039 0.939933 0.276656953
NR1H2 1582 OXYSTEROLS RECEPTOR LXR-BETA (LIVER X RECEPTOR BETA) (NUCLEAR ORPHAN RECEPTOR LXR-BETA) (UBIQUITOUSLY-EXPRESSED NUCLEAR RECEPTOR) (NUCLEAR RECEPTOR NER). [SWISSPROT;Acc:P55055] 0.0824164 0.34213 0.240892059
NR1H3 1579 OXYSTEROLS RECEPTOR LXR-ALPHA (LIVER X RECEPTOR ALPHA) (NUCLEAR ORPHAN RECEPTOR LXR-ALPHA). [SWISSPROT;Acc:Q13133] 0.110811 0.460002 0.240892431
NR2C1 1006 ORPHAN NUCLEAR RECEPTOR TR2. [SWISSPROT;Acc:P13056] 0.211877 0.831867 0.254700571
NR2E1 1007 ORPHAN NUCLEAR RECEPTOR NR2E1 (NUCLEAR RECEPTOR TLX) (TAILLESS HOMOLOG) (TLL) (HTLL). [SWISSPROT;Acc:Q9Y466] 0.280845 1.10266 0.254697731
NR4A1 2777 ORPHAN NUCLEAR RECEPTOR HMR (EARLY RESPONSE PROTEIN NAK1) (TR3 ORPHAN RECEPTOR). [SWISSPROT;Acc:P22736] 0.508993 2.52853 0.201299965
NR4A2 2775 ORPHAN NUCLEAR RECEPTOR NURR1 (IMMEDIATE-EARLY RESPONSE PROTEIN NOT) (TRANSCRIPTIONALLY INDUCIBLE NUCLEAR RECEPTOR). [SWISSPROT;Acc:P43354] 0.603026 2.99447 0.201379877
NR4A3 2776 NUCLEAR HORMONE RECEPTOR NOR-1 (NEURON-DERIVED ORPHAN RECEPTOR 1) (MITOGEN INDUCED NUCLEAR ORPHAN RECEPTOR). [SWISSPROT;Acc:Q92570] 0.515632 2.56143 0.201306302
NR6A1 907 ORPHAN NUCLEAR RECEPTOR NR6A1 (GERM CELL NUCLEAR FACTOR) (GCNF) (RETINOID RECEPTOR-RELATED TESTIS SPECIFIC RECEPTOR) (RTR). [SWISSPROT;Acc:Q15406] 0.196675 0.76137 0.258317244
NRD1 726 NARDILYSIN PRECURSOR (EC 3.4.24.61) (N-ARGININE DIBASIC CONVERTASE) (NRD CONVERTASE) (NRD-C). [SWISSPROT;Acc:O43847] 0.0787172 0.297409 0.26467659
NSF 1708 VESICLE-FUSING ATPASE (EC 3.6.4.6) (VESICULAR-FUSION PROTEIN NSF) (N- ETHYLMALEIMIDE SENSITIVE FUSION PROTEIN) (NEM-SENSITIVE FUSION PROTEIN). [SWISSPROT;Acc:P46459] 0.15883 0.66831 0.23765917
NSFL1C 675 P47 PROTEIN ISOFORM A. [RefSeq;Acc:NM_016143] 0.0978055 0.367477 0.266154072
NSMCE4A 3139 1.64337 25.135 0.065381739
NSUN2 2400 0.100955 0.460869 0.219053571
NSUN5 2399 WILLIAMS BEUREN SYNDROME CRITICAL REGION 20A ISOFORM 2; NOL1/NOP2/SUN GENE FAMILY MEMBER; WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY A; WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20. [RefSeq;Acc:NM_018044]
NSUN5B 2402 WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20C ISOFORM 1. [RefSeq;Acc:NM_032158] 0.0859883 0.392545 0.219053357
NUAK1 1004 PROBABLE SERINE/THREONINE-PROTEIN KINASE KIAA0537 (EC 2.7.1.-). [SWISSPROT;Acc:O60285] 0.139695 0.54802 0.25490858
NUAK2 998 0.115392 0.452671 0.254913613
NUBP1 2942 NUCLEOTIDE-BINDING PROTEIN 1 (NBP 1). [SWISSPROT;Acc:P53384] 0.0819552 0.528466 0.155081311
NUBP2 2943 NUCLEOTIDE BINDING PROTEIN 2 (NBP 2). [SWISSPROT;Acc:Q9Y5Y2]
NUCB1 2212 NUCLEOBINDIN 1 PRECURSOR (CALNUC). [SWISSPROT;Acc:Q02818] 0.0240186 0.106724 0.225053409
NUCB2 2210 NUCLEOBINDIN 2 PRECURSOR (DNA-BINDING PROTEIN NEFA). [SWISSPROT;Acc:P80303] 0.0283406 0.125928 0.225053999
NUDT12 1959 NUDIX (NUCLEOSIDE DIPHOSPHATE LINKED MOIETY X)-TYPE MOTIF 12. [RefSeq;Acc:NM_031438] 0.0196941 0.085173 0.231224684
NUDT21 359 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 5, 25 KD SUBUNIT; PRE-MRNA CLEAVAGE FACTOR IM (25KD); PRE-MRNA CLEAVAGE FACTOR IM, 25KD SUBUNIT. [RefSeq;Acc:NM_007006]" 0.288916 1.0267 0.281402552
NUFIP1 398 NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN INTERACTING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION INTERCATING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_012345] 0.0673151 0.241784 0.278410068
NUMB 2652 NUMB PROTEIN HOMOLOG (H-NUMB) (PROTEIN S171). [SWISSPROT;Acc:P49757] 0.130073 0.619508 0.209961776
NUMBL 2653 NUMB-LIKE PROTEIN (NUMB-R). [SWISSPROT;Acc:Q9Y6R0] 0.122765 0.584702 0.209961656
NUP43 1415 NUCLEOPORIN NUP43 (P42). [SWISSPROT;Acc:Q8NFH3] 0.149203 0.611499 0.243995493
NUP54 1480 NUCLEOPORIN 54KDA; NUCLEOPORIN P54. [RefSeq;Acc:NM_017426] 0.114912 0.472937 0.24297528
NUP88 310 NUCLEAR PORE COMPLEX PROTEIN NUP88 (NUCLEOPORIN NUP88) (88 KDA NUCLEAR PORE COMPLEX PROTEIN). [SWISSPROT;Acc:Q99567] 0.251667 0.851392 0.295594744

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/