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.


Navigation/Query Panel:
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 [...,...].
measured Hugo Gene description expected Rank final
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 3206 in total
measured
Hugo
description
expected
Rank
final
0.35534 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] 1.28928 457 0.275611194
0.355425 no value "ADENYLATE KINASE ISOENZYME 4, MITOCHONDRIAL (EC 2.7.4.3) (ATP-AMP TRANSPHOSPHORYLASE). [SWISSPROT;Acc:P27144]" 1.53719 1967 0.231217351
0.355846 PRKAB1 "5'-AMP-ACTIVATED PROTEIN KINASE, BETA-1 SUBUNIT (AMPK BETA-1 CHAIN) (AMPKB). [SWISSPROT;Acc:Q9Y478]" 1.13895 246 0.312433382
0.355858 ARPC1A ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 1A (SOP2-LIKE PROTEIN). [SWISSPROT;Acc:Q92747] 1.3445 724 0.264676832
0.35663 HNRPK HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K (HNRNP K) (DC-STRETCH BINDING PROTEIN) (CSBP) (TRANSFORMATION UPREGULATED NUCLEAR PROTEIN) (TUNP). [SWISSPROT;Acc:Q07244] 1.36939 860 0.260429826
0.356784 no value 1.28488 411 0.277678849
0.357172 N6AMT1 PUTATIVE N6-DNA-METHYLTRANSFERASE (EC 2.1.1.-) (PROTEIN PRED28) (M.HSAHEMK2P). [SWISSPROT;Acc:Q9Y5N5] 1.63578 2412 0.218349656
0.357744 ATP6V1B2 "VACUOLAR ATP SYNTHASE SUBUNIT B, BRAIN ISOFORM (EC 3.6.3.14) (V-ATPASE B2 SUBUNIT) (VACUOLAR PROTON PUMP B ISOFORM 2) (ENDOMEMBRANE PROTON PUMP 58 KDA SUBUNIT) (HO57). [SWISSPROT;Acc:P21281]" 1.51127 1744 0.236717463
0.357881 no value TRANSDUCIN-LIKE ENHANCER PROTEIN 1 (ESG1). [SWISSPROT;Acc:Q04724] 1.40331 995 0.255026331
0.35972 KPNB1 IMPORTIN BETA-1 SUBUNIT (KARYOPHERIN BETA-1 SUBUNIT) (NUCLEAR FACTOR P97) (IMPORTIN 90). [SWISSPROT;Acc:Q14974] 1.4749 1424 0.243894501
0.361623 EIF2S3 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 3 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 GAMMA SUBUNIT) (EIF-2-GAMMA). [SWISSPROT;Acc:P41091] 1.48057 1397 0.244245797
0.36177 SNRPD1 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1 (SNRNP CORE PROTEIN D1) (SM-D1) (SM-D AUTOANTIGEN). [SWISSPROT;Acc:P13641] 1.00996 123 0.358202305
0.363013 no value CBF1 INTERACTING COREPRESSOR. [RefSeq;Acc:NM_004882] 1.38457 787 0.262184649
0.363365 KCND2 "POTASSIUM VOLTAGE-GATED CHANNEL, SHAL-RELATED SUBFAMILY, MEMBER 2; VOLTAGE-SENSITIVE POTASSIUM CHANNEL; VOLTAGE-GATED POTASSIUM CHANNEL KV4.2. [RefSeq;Acc:NM_012281]" 1.46751 1243 0.24760649
0.363846 no value CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 1 (CKS-1) (SID1334) (PNAS-16 / PNAS-143). [SWISSPROT;Acc:P33551] 2.16723 2923 0.167885273
0.364089 CPSF4 "CLEAVAGE AND POLYADENYLATION SPECIFIC FACTOR 4, 30KD SUBUNIT; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR, 30KD; NO ARCHES-LIKE (ZEBRAFISH) ZINC FINGER PROTEIN; CLEAVAGE-POLYADENYLATION SPECIFICITY FACTOR. [RefSeq;Acc:NM_006693]" 1.77759 2741 0.204821697
0.364125 ERCC5 DNA-REPAIR PROTEIN COMPLEMENTING XP-G CELLS (XERODERMA PIGMENTOSUM GROUP G COMPLEMENTING PROTEIN) (DNA EXCISION REPAIR PROTEIN ERCC-5). [SWISSPROT;Acc:P28715] 0.853699 25 0.426526211
0.365106 OSGEPL1 PUTATIVE SIALOGLYCOPROTEASE TYPE 2. [RefSeq;Acc:NM_022353] 1.55176 1783 0.235285096
0.365822 no value RAN-BINDING PROTEIN 2-LIKE 1 ISOFORM 2; SPERM MEMBRANE PROTEIN BS-63; RAN-BINDING PROTEIN 2-LIKE 1. [RefSeq;Acc:NM_032260] 1.365 648 0.268001465
0.366149 CPSF2 "CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 100 KDA SUBUNIT (CPSF 100 KDA SUBUNIT) (FRAGMENT). [SWISSPROT;Acc:Q9P2I0]" 1.78474 2740 0.205155373
0.366428 ATP5B "ATP SYNTHASE BETA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P06576]" 1.64277 2262 0.223054962
0.366443 NME3 NUCLEOSIDE DIPHOSPHATE KINASE 3 (EC 2.7.4.6) (NDK 3) (NDP KINASE 3) (NM23-H3) (DR-NM23). [SWISSPROT;Acc:Q13232] 1.59695 2065 0.229464291
0.367035 EIF3D EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 7 (EIF-3 ZETA) (EIF3 P66) (EIF3D). [SWISSPROT;Acc:O15371] 1.33921 503 0.274068294
0.367121 PFKP "6-PHOSPHOFRUCTOKINASE, TYPE C (EC 2.7.1.11) (PHOSPHOFRUCTOKINASE 1) (PHOSPHOHEXOKINASE) (PHOSPHOFRUCTO-1-KINASE ISOZYME C) (PFK-C) (6-PHOSPHOFRUCTOKINASE, PLATELET TYPE). [SWISSPROT;Acc:Q01813]" 2.42367 2949 0.151473179
0.367472 DIMT1L "PROBABLE DIMETHYLADENOSINE TRANSFERASE (EC 2.1.1.-) (S- ADENOSYLMETHIONINE-6-N',N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE) (18S RRNA DIMETHYLASE). [SWISSPROT;Acc:Q9UNQ2]" 1.54946 1722 0.237161334
0.368426 FNBP1L 1.32182 391 0.278726302
0.368948 SFRS10 ARGININE/SERINE-RICH SPLICING FACTOR 10 (TRANSFORMER-2-BETA) (HTRA2- BETA) (TRANSFORMER 2 PROTEIN HOMOLOG) (SILICA-INDUCED PROTEIN 41) (RA301). [SWISSPROT;Acc:Q15815] 1.32916 412 0.277579825
0.369521 ISL2 INSULIN GENE ENHANCER PROTEIN ISL-2 (ISLET-2). [SWISSPROT;Acc:Q96A47] 1.8374 2779 0.201110809
0.37085 MAD2L1 MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A (MAD2-LIKE 1) (HSMAD2). [SWISSPROT;Acc:Q13257] 1.49174 1190 0.248602303
0.374541 SF3A2 SPLICING FACTOR 3A SUBUNIT 2 (SPLICEOSOME ASSOCIATED PROTEIN 62) (SAP 62) (SF3A66). [SWISSPROT;Acc:Q15428] 1.24681 298 0.300399419
0.374769 TIAL1 NUCLEOLYSIN TIAR (TIA-1 RELATED PROTEIN). [SWISSPROT;Acc:Q01085] 1.03782 119 0.361111753
0.374874 LHX4 LIM/HOMEOBOX PROTEIN LHX4. [SWISSPROT;Acc:Q969G2] 1.63637 2078 0.229088776
0.375086 no value UBA/UBX 33.3 KDA PROTEIN. [SWISSPROT;Acc:Q04323] 1.05643 126 0.3550505
0.375423 DCTN2 DYNACTIN COMPLEX 50 KDA SUBUNIT (50 KDA DYNEIN-ASSOCIATED POLYPEPTIDE) (DYNAMITIN) (DCTN-50) (DYNACTIN 2). [SWISSPROT;Acc:Q13561] 1.57827 1694 0.237869946
0.375556 EIF5 EUKARYOTIC TRANSLATION INITIATION FACTOR 5 (EIF-5). [SWISSPROT;Acc:P55010] 0.956345 84 0.392699287
0.376553 EIF5AP1 EUKARYOTIC TRANSLATION INITIATION FACTOR 5A (EIF-5A) (EIF-4D) (REV- BINDING FACTOR). [SWISSPROT;Acc:P10159] 1.56403 1586 0.24075817
0.377523 PAPOLG POLY(A) POLYMERASE GAMMA (EC 2.7.7.19) (PAP GAMMA) (POLYNUCLEOTIDE ADENYLYLTRANSFERASE GAMMA) (SRP RNA 3' ADENYLATING ENZYME). [SWISSPROT;Acc:Q9BWT3] 1.81111 2680 0.20844841
0.378587 DLGAP1 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] 0.920789 56 0.411154999
DLGAP4 DISKS LARGE-ASSOCIATED PROTEIN 4 (DAP-4) (SAP90/PSD-95-ASSOCIATED PROTEIN 4) (SAPAP4) (PSD-95/SAP90 BINDING PROTEIN 4). [SWISSPROT;Acc:Q9Y2H0] 57
0.378654 TATDN1 CDA11 PROTEIN. [RefSeq;Acc:NM_032026] 1.60733 1777 0.235579501
0.379284 VAV1 VAV PROTO-ONCOGENE. [SWISSPROT;Acc:P15498] 1.01082 98 0.375224076
0.379312 UFD1L UBIQUITIN FUSION DEGRADATION PROTEIN 1 HOMOLOG (UB FUSION PROTEIN 1). [SWISSPROT;Acc:Q92890] 1.35854 374 0.279205618
0.379831 SETMAR SET DOMAIN AND MARINER TRANSPOSASE FUSION GENE. [RefSeq;Acc:NM_006515] 3.11762 3014 0.121833642
0.380273 VAV3 VAV-3 PROTEIN. [SWISSPROT;Acc:Q9UKW4] 1.015 99 0.374653202
0.38076 PDHA1 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, SOMATIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE I). [SWISSPROT;Acc:P08559]" 1.65321 2025 0.230315568
0.381101 no value DJ470L14.3 (NOVEL PROTEIN SIMILAR TO THE ARP2/3 PROTEIN COMPLEX SUBUNIT P21-ARC (ARC21)). [SPTREMBL;Acc:Q9H5B6] 1.43987 721 0.264677367
0.382713 ERCC2 TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX HELICASE SUBUNIT (EC 3.6.1.-) (DNA-REPAIR PROTEIN COMPLEMENTING XP-D CELLS) (XERODERMA PIGMENTOSUM GROUP D COMPLEMENTING PROTEIN) (CXPD) (DNA EXCISION REPAIR PROTEIN ERCC-2). [SWISSPROT;Acc:P18074] 1.87606 2750 0.203998273
0.383112 TAF9B "TBP-ASSOCIATED FACTOR 9L; NEURONAL CELL DEATH-RELATED PROTEIN; TAF9-LIKE RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 31 KD; NEURONAL CELL DEATH-RELATED GENE IN NEURON-7; TRANSCRIPTION ASSOCIATED FACTOR TAFII31L; TRANSCRIPTION INIT" 1.83532 2675 0.208743979
0.383414 WDR3 WD-REPEAT PROTEIN 3. [SWISSPROT;Acc:Q9UNX4] 1.57686 1454 0.243150311
0.383439 ATP5A1 "ATP SYNTHASE ALPHA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.3.14). [SWISSPROT;Acc:P25705]" 1.79234 2562 0.213932066

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/