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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expected Gene Rank description measured final Hugo
Results: HTML CSV LaTeX Showing element 2352 to 2401 of 3206 in total
expected
Rank
description
measured
final
Hugo
1.06765 2297 SORTING NEXIN 9 (SH3 AND PX DOMAIN-CONTAINING PROTEIN 1) (SDP1 PROTEIN). [SWISSPROT;Acc:Q9Y5X1] 0.237383 0.222341591 SNX9
1.06793 3155 MELANOMA-ASSOCIATED ANTIGEN F1 (MAGE-F1 ANTIGEN). [SWISSPROT;Acc:Q9HAY2] 0.0698227 0.065381345 MAGEF1
1.06873 1805 GTP CYCLOHYDROLASE I (EC 3.5.4.16) (GTP-CH-I). [SWISSPROT;Acc:P30793] 0.250702 0.234579361 GCH1
1.07259 1281 CATHEPSIN B PRECURSOR (EC 3.4.22.1) (CATHEPSIN B1) (APP SECRETASE). [SWISSPROT;Acc:P07858] 0.264212 0.246330844 CTSB
1.07305 1228 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN M (HNRNP M). [SWISSPROT;Acc:P52272] 0.266011 0.247901775 HNRPM
1.0738 760 TUMOR ENDOTHELIAL MARKER 6; THYROID SPECIFIC PTB DOMAIN PROTEIN; TENSIN 3. [RefSeq;Acc:NM_022748] 0.283226 0.263760477 TNS3
1.07406 1271 0.264834 0.246572817 no value
1.08199 2681 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 INTERACTING PROTEIN 1 (TAK1-BINDING PROTEIN 1). [SWISSPROT;Acc:Q15750] 0.225506 0.208417823 MAP3K7IP1
1.08201 2173 NUCLEAR PORE COMPLEX PROTEIN NUP98 (NUCLEOPORIN NUP98) (98 KDA NUCLEOPORIN). [SWISSPROT;Acc:P52948] 0.245551 0.226939677 NUP98
1.08227 2926 "MALATE DEHYDROGENASE, MITOCHONDRIAL PRECURSOR (EC 1.1.1.37). [SWISSPROT;Acc:P40926]" 0.177425 0.163937834 MDH2
1.0823 2206 PROTEIN CDC27HS (CELL DIVISION CYCLE PROTEIN 27 HOMOLOG) (H-NUC). [SWISSPROT;Acc:P30260] 0.244035 0.225478148 CDC27
1.08234 1664 CYCLIN M3; ANCIENT CONSERVED DOMAIN PROTEIN 3. [RefSeq;Acc:NM_017623] 0.258494 0.238828834 CNNM3
1.08675 923 HEAT SHOCK 27 KDA PROTEIN (HSP 27) (STRESS-RESPONSIVE PROTEIN 27) (SRP27) (ESTROGEN-REGULATED 24 KDA PROTEIN) (28 KDA HEAT SHOCK PROTEIN). [SWISSPROT;Acc:P04792] 0.28007 0.257713366 HSPB1
1.08705 3007 0.136179 0.125273906 SEPT11
1.09266 1301 RAC GTPASE ACTIVATING PROTEIN 1; GTPASE ACTIVATING PROTEIN. [RefSeq;Acc:NM_013277] 0.268542 0.245769041 RACGAP1
1.09378 2499 "MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 3.4.24.64) (ALPHA-MPP) (P-55) (HA1523). [SWISSPROT;Acc:Q10713]" 0.235517 0.215323923 PMPCA
1.09489 65 DNA POLYMERASE EPSILON P17 SUBUNIT (DNA POLYMERASE EPSILON SUBUNIT 3) (CHROMATIN ACCESSIBILITY COMPLEX 17) (HUCHRAC17) (CHRAC-17). [SWISSPROT;Acc:Q9NRF9] 0.446035 0.407378823 POLE3
1.09519 1236 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L1. [SWISSPROT;Acc:P28370] 0.271278 0.247699486 SMARCA1
1.09557 3031 0.128895 0.117651086 PTCD1
1.09872 1319 0.269894 0.245644022 ARD1B
1.09904 124 SON OF SEVENLESS PROTEIN HOMOLOG 1 (SOS-1). [SWISSPROT;Acc:Q07889] 0.393069 0.357647583 SOS1
1.10102 971 SUPPRESSOR OF ACTIN MUTATIONS 2-LIKE ISOFORM B; DJ1033B10.5. [RefSeq;Acc:NM_022553] 0.281375 0.255558482 VPS52
1.10122 278 "OLIGOPEPTIDE TRANSPORTER, KIDNEY ISOFORM (PEPTIDE TRANSPORTER 2) (KIDNEY H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 2). [SWISSPROT;Acc:Q16348]" 0.33474 0.303971958 SLC15A2
1.10266 1007 ORPHAN NUCLEAR RECEPTOR NR2E1 (NUCLEAR RECEPTOR TLX) (TAILLESS HOMOLOG) (TLL) (HTLL). [SWISSPROT;Acc:Q9Y466] 0.280845 0.254697731 NR2E1
1.10466 305 0.329649 0.298416707 ATG16L2
1.10501 1672 "SPLICING FACTOR, PROLINE-AND GLUTAMINE-RICH (POLYPYRIMIDINE TRACT- BINDING PROTEIN-ASSOCIATED SPLICING FACTOR) (PTB-ASSOCIATED SPLICING FACTOR) (PSF) (DNA-BINDING P52/P100 COMPLEX, 100 KDA SUBUNIT). [SWISSPROT;Acc:P23246]" 0.263446 0.238410512 SFPQ
1.10619 993 AFG3-LIKE PROTEIN 2 (EC 3.4.24.-) (PARAPLEGIN-LIKE PROTEIN). [SWISSPROT;Acc:Q9Y4W6] 0.282136 0.255052025 AFG3L2
1.10654 2491 DEHYDRODOLICHYL DIPHOSPHATE SYNTHASE. [RefSeq;Acc:NM_024887] 0.238591 0.215618956 DHDDS
1.10693 1345 PROBABLE RRNA PROCESSING PROTEIN EBP2 (EBNA1 BINDING PROTEIN 2) (NUCLEOLAR PROTEIN P40). [SWISSPROT;Acc:Q99848] 0.271421 0.245201594 EBNA1BP2
1.10704 1326 ENHANCER OF RUDIMENTARY HOMOLOG. [SWISSPROT;Acc:Q14259] 0.271803 0.245522294 ERH
1.10767 1663 CYCLIN M1; ANCIENT CONSERVED DOMAIN PROTEIN 1. [RefSeq;Acc:NM_020348] 0.264548 0.238832865 CNNM1
1.10792 1021 "FTSJ HOMOLOG 3; LIKELY ORTHOLOG OF MOUSE ECTOPLACENTAL CONE, INVASIVE TROPHOBLAST GIANT CELLS, EXTRAEMBRYONIC ECTODERM AND CHORION SEQUENCE 3. [RefSeq;Acc:NM_017647]" 0.280943 0.253576973 FTSJ3
1.10989 111 NUCLEOLYSIN TIA-1 (RNA-BINDING PROTEIN TIA-1) (P40-TIA-1) [CONTAINS: P15-TIA-1]. [SWISSPROT;Acc:P31483] 0.401253 0.361525016 TIA1
1.11021 990 HOMEOBOX PROTEIN ENGRAILED-2 (HU-EN-2). [SWISSPROT;Acc:P19622] 0.283289 0.25516704 EN2
1.11055 467 "STERILE ALPHA AND TIR MOTIF CONTAINING 1; STERILE ALPHA AND HEAT/ARMADILLO MOTIF PROTEIN, ORTHOLOG OF DROSOPHILA. [RefSeq;Acc:NM_015077]" 0.305359 0.274961956 SARM1
1.11109 2492 0.239571 0.215617997 no value
1.11156 1143 POLYMERASE DELTA-INTERACTING PROTEIN 1; TNFAIP1-LIKE. [RefSeq;Acc:NM_178863] 0.278202 0.250280687 KCTD13
1.11232 2117 HYDROXYINDOLE O-METHYLTRANSFERASE (EC 2.1.1.4) (HIOMT) (ACETYLSEROTONIN O-METHYLTRANSFERASE) (ASMT). [SWISSPROT;Acc:P46597] 0.253802 0.228173547 no value
1.11332 3161 "MYOSIN HEAVY CHAIN, SKELETAL MUSCLE, EXTRAOCULAR (MYHC-EO). [SWISSPROT;Acc:Q9UKX3]" 0.0720434 0.064710416 MYH13
1.11347 1473 SURVIVAL MOTOR NEURON PROTEIN (COMPONENT OF GEMS 1) (GEMIN1). [SWISSPROT;Acc:Q16637] 0.270547 0.242976461 no value
1.11415 1075 TAX INTERACTION PROTEIN 1. [RefSeq;Acc:NM_014604] 0.281064 0.252267648
1.11536 2389 "SUCCINYL-COA LIGASE [GDP-FORMING] ALPHA-CHAIN, MITOCHONDRIAL PRECURSOR (EC 6.2.1.4) (SUCCINYL-COA SYNTHETASE, ALPHA CHAIN) (SCS-ALPHA). [SWISSPROT;Acc:P53597]" 0.245024 0.219681538 SUCLG1
2390 "SUCCINYL-COA LIGASE [ADP-FORMING] BETA-CHAIN, MITOCHONDRIAL PRECURSOR (EC 6.2.1.5) (SUCCINYL-COA SYNTHETASE, BETAA CHAIN) (SCS-BETAA) (ATP- SPECIFIC SUCCINYL-COA SYNTHETASE BETA SUBUNIT). [SWISSPROT;Acc:Q9P2R7]" SUCLA2
1.11593 1029 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE M2 CHAIN (EC 1.17.4.1) (RIBONUCLEOTIDE REDUCTASE SMALL CHAIN). [SWISSPROT;Acc:P31350] 0.282811 0.253430771 RRM2
1.11741 358 PROTEIN AD-016 (PROTEIN CGI-116) (X0009). [SWISSPROT;Acc:Q9Y3C0] 0.3145 0.281454435 CCDC53
1.12068 3036 GABA(A) RECEPTOR-ASSOCIATED PROTEIN; GABA(A)-RECEPTOR-ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007278] 0.125771 0.112227398 GABARAP
1.12113 2285 DNA-DIRECTED RNA POLYMERASE II 13.3 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB11). [SWISSPROT;Acc:P52435] 0.249308 0.222372071 POLR2J
1.12158 2855 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE GAMMA (EC 2.3.1.51) (1- AGP ACYLTRANSFERASE 3) (1-AGPAT 3) (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE-GAMMA) (LPAAT-GAMMA) (1-ACYLGLYCEROL-3-PHOSPHATE O- ACYLTRANSFERASE 3). [SWISSPROT;Acc:Q9NRZ7] 0.214138 0.190925302 AGPAT3
1.12271 1063 PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-3 (HOMEOBOX PROTEIN PBX3). [SWISSPROT;Acc:P40426] 0.283637 0.252636032 PBX3
1.12415 905 SIMILAR TO GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE (HYPOTHETICAL PROTEIN FLJ33258). [SPTREMBL;Acc:Q96EK6] 0.29051 0.258426367 GNPNAT1

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/